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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1060500387

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr17:31358566-31358569 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
delAG
Variation Type
Indel Insertion and Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
NF1 : Frameshift
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 17 NC_000017.11:g.31358566_31358567[1]
GRCh37.p13 chr 17 NC_000017.10:g.29685584_29685585[1]
NF1 RefSeqGene (LRG_214) NG_009018.1:g.268590_268591[1]
Gene: NF1, neurofibromin 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NF1 transcript variant 3 NM_001128147.2:c. N/A Genic Downstream Transcript Variant
NF1 transcript variant 2 NM_000267.3:c.799...

NM_000267.3:c.7994_7995[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform 2 NP_000258.1:p.Ser...

NP_000258.1:p.Ser2666fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant 1 NM_001042492.2:c....

NM_001042492.2:c.8057_8058[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform 1 NP_001035957.1:p....

NP_001035957.1:p.Ser2687fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X10 XM_017024690.1:c. N/A Genic Downstream Transcript Variant
NF1 transcript variant X1 XM_006721922.2:c....

XM_006721922.2:c.8087_8088[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X1 XP_006721985.1:p....

XP_006721985.1:p.Ser2697fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X2 XM_011524852.2:c....

XM_011524852.2:c.8084_8085[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X2 XP_011523154.1:p....

XP_011523154.1:p.Ser2696fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X3 XM_005257983.2:c....

XM_005257983.2:c.8057_8058[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X3 XP_005258040.1:p....

XP_005258040.1:p.Ser2687fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X4 XM_006721924.2:c....

XM_006721924.2:c.8087_8088[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X4 XP_006721987.1:p....

XP_006721987.1:p.Ser2697fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X5 XM_006721925.2:c....

XM_006721925.2:c.8024_8025[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X5 XP_006721988.1:p....

XP_006721988.1:p.Ser2676fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X6 XM_005257984.2:c....

XM_005257984.2:c.7994_7995[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X6 XP_005258041.1:p....

XP_005258041.1:p.Ser2666fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X7 XM_017024689.1:c....

XM_017024689.1:c.8024_8025[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X7 XP_016880178.1:p....

XP_016880178.1:p.Ser2676fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X8 XM_011524857.2:c....

XM_011524857.2:c.7964_7965[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X8 XP_011523159.1:p....

XP_011523159.1:p.Ser2656fs

S (Ser) > C (Cys) Frameshift
NF1 transcript variant X9 XM_006721926.3:c....

XM_006721926.3:c.8087_8088[1]

S [AGT] > C [T] Coding Sequence Variant
neurofibromin isoform X9 XP_006721989.1:p....

XP_006721989.1:p.Ser2697fs

S (Ser) > C (Cys) Frameshift
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: delAG (allele ID: 402548 )
ClinVar Accession Disease Names Clinical Significance
RCV000471092.2 Neurofibromatosis, type 1 Pathogenic
RCV000492474.1 Hereditary cancer-predisposing syndrome Pathogenic
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

None
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement AGAG= delAG Note
GRCh38.p7 chr 17 NC_000017.11:g.31358566...

NC_000017.11:g.31358566_31358569AGAG=

NC_000017.11:g.31358566...

NC_000017.11:g.31358566_31358567[1]

GRCh37.p13 chr 17 NC_000017.10:g.29685584...

NC_000017.10:g.29685584_29685587AGAG=

NC_000017.10:g.29685584...

NC_000017.10:g.29685584_29685585[1]

NF1 RefSeqGene (LRG_214) NG_009018.1:g.268590_26...

NG_009018.1:g.268590_268593AGAG=

NG_009018.1:g.268590_26...

NG_009018.1:g.268590_268591[1]

NF1 transcript variant 2 NM_000267.3:c.7994_7997...

NM_000267.3:c.7994_7997AGAG=

NM_000267.3:c.7994_7995[1]
NF1 transcript variant 1 NM_001042492.2:c.8057_8...

NM_001042492.2:c.8057_8060AGAG=

NM_001042492.2:c.8057_8...

NM_001042492.2:c.8057_8058[1]

NF1 transcript variant X9 XM_006721926.3:c.8087_8...

XM_006721926.3:c.8087_8090AGAG=

XM_006721926.3:c.8087_8...

XM_006721926.3:c.8087_8088[1]

NF1 transcript variant X1 XM_006721922.2:c.8087_8...

XM_006721922.2:c.8087_8090AGAG=

XM_006721922.2:c.8087_8...

XM_006721922.2:c.8087_8088[1]

NF1 transcript variant X2 XM_011524852.2:c.8084_8...

XM_011524852.2:c.8084_8087AGAG=

XM_011524852.2:c.8084_8...

XM_011524852.2:c.8084_8085[1]

NF1 transcript variant X3 XM_005257983.2:c.8057_8...

XM_005257983.2:c.8057_8060AGAG=

XM_005257983.2:c.8057_8...

XM_005257983.2:c.8057_8058[1]

NF1 transcript variant X3 XM_005257983.1:c.8057_8...

XM_005257983.1:c.8057_8060AGAG=

XM_005257983.1:c.8057_8...

XM_005257983.1:c.8057_8058[1]

NF1 transcript variant X4 XM_006721924.2:c.8087_8...

XM_006721924.2:c.8087_8090AGAG=

XM_006721924.2:c.8087_8...

XM_006721924.2:c.8087_8088[1]

NF1 transcript variant X5 XM_006721925.2:c.8024_8...

XM_006721925.2:c.8024_8027AGAG=

XM_006721925.2:c.8024_8...

XM_006721925.2:c.8024_8025[1]

NF1 transcript variant X6 XM_005257984.2:c.7994_7...

XM_005257984.2:c.7994_7997AGAG=

XM_005257984.2:c.7994_7...

XM_005257984.2:c.7994_7995[1]

NF1 transcript variant X11 XM_005257984.1:c.7994_7...

XM_005257984.1:c.7994_7997AGAG=

XM_005257984.1:c.7994_7...

XM_005257984.1:c.7994_7995[1]

NF1 transcript variant X8 XM_011524857.2:c.7964_7...

XM_011524857.2:c.7964_7967AGAG=

XM_011524857.2:c.7964_7...

XM_011524857.2:c.7964_7965[1]

NF1 transcript variant X7 XM_017024689.1:c.8024_8...

XM_017024689.1:c.8024_8027AGAG=

XM_017024689.1:c.8024_8...

XM_017024689.1:c.8024_8025[1]

neurofibromin isoform 2 NP_000258.1:p.Gln2665_S...

NP_000258.1:p.Gln2665_Ser2666=

NP_000258.1:p.Ser2666fs
neurofibromin isoform 1 NP_001035957.1:p.Gln268...

NP_001035957.1:p.Gln2686_Ser2687=

NP_001035957.1:p.Ser2687fs
neurofibromin isoform X9 XP_006721989.1:p.Gln269...

XP_006721989.1:p.Gln2696_Ser2697=

XP_006721989.1:p.Ser2697fs
neurofibromin isoform X1 XP_006721985.1:p.Gln269...

XP_006721985.1:p.Gln2696_Ser2697=

XP_006721985.1:p.Ser2697fs
neurofibromin isoform X2 XP_011523154.1:p.Gln269...

XP_011523154.1:p.Gln2695_Ser2696=

XP_011523154.1:p.Ser2696fs
neurofibromin isoform X3 XP_005258040.1:p.Gln268...

XP_005258040.1:p.Gln2686_Ser2687=

XP_005258040.1:p.Ser2687fs
neurofibromin isoform X4 XP_006721987.1:p.Gln269...

XP_006721987.1:p.Gln2696_Ser2697=

XP_006721987.1:p.Ser2697fs
neurofibromin isoform X5 XP_006721988.1:p.Gln267...

XP_006721988.1:p.Gln2675_Ser2676=

XP_006721988.1:p.Ser2676fs
neurofibromin isoform X6 XP_005258041.1:p.Gln266...

XP_005258041.1:p.Gln2665_Ser2666=

XP_005258041.1:p.Ser2666fs
neurofibromin isoform X8 XP_011523159.1:p.Gln265...

XP_011523159.1:p.Gln2655_Ser2656=

XP_011523159.1:p.Ser2656fs
neurofibromin isoform X7 XP_016880178.1:p.Gln267...

XP_016880178.1:p.Gln2675_Ser2676=

XP_016880178.1:p.Ser2676fs
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

1 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss2137511577 May 05, 2017 (150)
2 ClinVar RCV000471092.2 Jul 20, 2018 (151)
3 ClinVar RCV000492474.1 Jul 20, 2018 (151)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
RCV000471092.2, RCV000492474.1, ss2137511577 NC_000017.11:31358567:delAG NC_000017.11:31358565:delAG (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1060500387

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e