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dbSNP Short Genetic Variations

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.


Current Build 151

Released July 17, 2018

Homo sapiens
chrX:21743783-21743788 (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.

delG / dupG
Variation Type
Indel Insertion and Deletion
Clinical Significance
Reported in ClinVar
Gene : Consequence
SMPX : Frameshift
1 citation
Genomic View
See rs on genome

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 X NC_000023.11:g.21743788delG
GRCh38.p7 chr X NC_000023.11:g.21743788dup
GRCh37.p13 chr X NC_000023.10:g.21761906delG
GRCh37.p13 chr X NC_000023.10:g.21761906dup
SMPX RefSeqGene NG_031916.1:g.19378delC
SMPX RefSeqGene NG_031916.1:g.19378dup
Gene: SMPX, small muscle protein, X-linked (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SMPX transcript variant 1 NM_014332.2:c.99delC P [CCC] > P [CC] Coding Sequence Variant
small muscular protein NP_055147.1:p.Pro...


P (Pro) > P (Pro) Frameshift
SMPX transcript variant 1 NM_014332.2:c.99dup R [AGA] > Q [CAGA] Coding Sequence Variant
small muscular protein NP_055147.1:p.Arg...


R (Arg) > Q (Gln) Frameshift
SMPX transcript variant 2 NR_045617.1:n.330...


N/A Non Coding Transcript Variant
SMPX transcript variant 2 NR_045617.1:n.330dup N/A Non Coding Transcript Variant

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: delG (allele ID: 48574 )
ClinVar Accession Disease Names Clinical Significance
RCV000033153.12 Deafness, X-linked 4 Pathogenic
Allele: dupG (allele ID: 438925 )
ClinVar Accession Disease Names Clinical Significance
RCV000514049.1 not provided Likely-Pathogenic

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").

Study Population Group Sample Size Ref Allele Alt Allele
The Exome Aggregation Consortium Global Study-wide 87544 -

No frequency provided

The Exome Aggregation Consortium Europe Sub 52410 -

No frequency provided

The Exome Aggregation Consortium Asian Sub 16720 -

No frequency provided

The Exome Aggregation Consortium American Sub 9272 -

No frequency provided

The Exome Aggregation Consortium African Sub 8512 -

No frequency provided

The Exome Aggregation Consortium Other Sub 630 -

No frequency provided


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 (G)6= delG dupG Note
GRCh38.p7 chr X NC_000023.11:g.21...






GRCh37.p13 chr X NC_000023.10:g.21...






SMPX RefSeqGene NG_031916.1:g.193...






SMPX transcript variant 1 NM_014332.2:c.94_...


NM_014332.2:c.99delC NM_014332.2:c.99dup
SMPX transcript variant 2 NR_045617.1:n.325...




small muscular protein NP_055147.1:p.Pro...







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 ClinVar, 1 Frequency, 2 SubSNP submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss947429118 Jan 10, 2014 (138)
2 EVA_EXAC ss1712260600 Apr 01, 2015 (144)
3 The Exome Aggregation Consortium NC_000023.10 - 21761901 Jul 20, 2018 (151)
4 ClinVar RCV000033153.12 Jul 20, 2018 (151)
5 ClinVar RCV000514049.1 Jul 20, 2018 (151)

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
RCV000033153.12, ss947429118 NC_000023.11:21743782:delG NC_000023.11:21743782:delG (self)
9973437, ss1712260600 NC_000023.10:21761900:insG NC_000023.11:21743782:dupG rs755269700
RCV000514049.1 NC_000023.11:21743782:insG NC_000023.11:21743782:dupG

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

1 citation for rs398122930
PMID Title Author Year Journal
22911656 A novel deletion in SMPX causes a rare form of X-linked progressive hearing loss in two families due to a founder effect. Abdelfatah N et al. 2013 Human mutation

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