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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

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.

rs764177294

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:33301573-33301577 (GRCh38.p14) 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
delCTT
Variation Type
Indel Insertion and Deletion
Frequency
delCTT=0.000004 (1/245816, GnomAD_exome)
delCTT=0.000009 (1/110696, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CEBPA : Inframe Deletion
CEBPA-DT : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 245816 TTCTT=0.999996 delCTT=0.000004
gnomAD - Exomes European Sub 131518 TTCTT=0.999992 delCTT=0.000008
gnomAD - Exomes Asian Sub 48408 TTCTT=1.00000 delCTT=0.00000
gnomAD - Exomes American Sub 34354 TTCTT=1.00000 delCTT=0.00000
gnomAD - Exomes African Sub 15562 TTCTT=1.00000 delCTT=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9972 TTCTT=1.0000 delCTT=0.0000
gnomAD - Exomes Other Sub 6002 TTCTT=1.0000 delCTT=0.0000
ExAC Global Study-wide 110696 TTCTT=0.999991 delCTT=0.000009
ExAC Europe Sub 66938 TTCTT=0.99999 delCTT=0.00001
ExAC Asian Sub 23428 TTCTT=1.00000 delCTT=0.00000
ExAC American Sub 10538 TTCTT=1.00000 delCTT=0.00000
ExAC African Sub 8968 TTCTT=1.0000 delCTT=0.0000
ExAC Other Sub 824 TTCTT=1.000 delCTT=0.000
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.p14 chr 19 NC_000019.10:g.33301575_33301577del
GRCh37.p13 chr 19 NC_000019.9:g.33792481_33792483del
CEBPA RefSeqGene (LRG_456) NG_012022.1:g.5950_5952del
Gene: CEBPA, CCAAT enhancer binding protein alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEBPA transcript variant 1 NM_001287424.2:c.945_947d…

NM_001287424.2:c.945_947del

K [AAGA] > [AAC] Coding Sequence Variant
CCAAT/enhancer-binding protein alpha isoform c NP_001274353.1:p.Lys315del K (Lys) > () Inframe Deletion
CEBPA transcript variant 1 NM_004364.5:c.840_842del K [AAGA] > [AAC] Coding Sequence Variant
CCAAT/enhancer-binding protein alpha isoform a NP_004355.2:p.Lys280del K (Lys) > () Inframe Deletion
CEBPA transcript variant 1 NM_001285829.2:c.483_485d…

NM_001285829.2:c.483_485del

K [AAGA] > [AAC] Coding Sequence Variant
CCAAT/enhancer-binding protein alpha isoform b NP_001272758.1:p.Lys161del K (Lys) > () Inframe Deletion
CEBPA transcript variant 1 NM_001287435.2:c.798_800d…

NM_001287435.2:c.798_800del

K [AAGA] > [AAC] Coding Sequence Variant
CCAAT/enhancer-binding protein alpha isoform d NP_001274364.1:p.Lys266del K (Lys) > () Inframe Deletion
Gene: CEBPA-DT, CEBPA divergent transcript (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CEBPA-DT transcript NR_026887.2:n. N/A Upstream Transcript Variant
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.

Not Reported in ClinVar
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 TTCTT= delCTT
GRCh38.p14 chr 19 NC_000019.10:g.33301573_33301577= NC_000019.10:g.33301575_33301577del
GRCh37.p13 chr 19 NC_000019.9:g.33792479_33792483= NC_000019.9:g.33792481_33792483del
CEBPA RefSeqGene (LRG_456) NG_012022.1:g.5948_5952= NG_012022.1:g.5950_5952del
CEBPA transcript variant 1 NM_004364.5:c.838_842= NM_004364.5:c.840_842del
CEBPA transcript variant 1 NM_004364.4:c.838_842= NM_004364.4:c.840_842del
CEBPA transcript NM_004364.3:c.838_842= NM_004364.3:c.840_842del
CEBPA transcript variant 1 NM_001287435.2:c.796_800= NM_001287435.2:c.798_800del
CEBPA transcript variant 1 NM_001287435.1:c.796_800= NM_001287435.1:c.798_800del
CEBPA transcript variant 1 NM_001287424.2:c.943_947= NM_001287424.2:c.945_947del
CEBPA transcript variant 1 NM_001287424.1:c.943_947= NM_001287424.1:c.945_947del
CEBPA transcript variant 1 NM_001285829.2:c.481_485= NM_001285829.2:c.483_485del
CEBPA transcript variant 1 NM_001285829.1:c.481_485= NM_001285829.1:c.483_485del
CCAAT/enhancer-binding protein alpha isoform a NP_004355.2:p.Lys280_Asn281= NP_004355.2:p.Lys280del
CCAAT/enhancer-binding protein alpha isoform d NP_001274364.1:p.Lys266_Asn267= NP_001274364.1:p.Lys266del
CCAAT/enhancer-binding protein alpha isoform c NP_001274353.1:p.Lys315_Asn316= NP_001274353.1:p.Lys315del
CCAAT/enhancer-binding protein alpha isoform b NP_001272758.1:p.Lys161_Asn162= NP_001272758.1:p.Lys161del
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#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1712196021 Apr 01, 2015 (144)
2 GNOMAD ss2743876224 Nov 08, 2017 (151)
3 ExAC NC_000019.9 - 33792479 Oct 12, 2018 (152)
4 gnomAD - Exomes NC_000019.9 - 33792479 Jul 13, 2019 (153)
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
4025657, 13189803, ss1712196021, ss2743876224 NC_000019.9:33792478:TTC: NC_000019.10:33301572:TTCTT:TT (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 rs764177294

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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: 2.0.1.post761+d5e8e07