rs3014836

Variant names:

• chr1-153458724-T-A
• rs3014836
• NM_002963.4:c.141+149A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-153458724-T-A
• chr1-153458724-T-C
• chr1-153458724-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002963.4(S100A7):​c.141+149A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: S100A7 NM_002963.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 3 publications found

Genes affected

S100A7 (HGNC:10497): (S100 calcium binding protein A7) The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein differs from the other S100 proteins of known structure in its lack of calcium binding ability in one EF-hand at the N-terminus. The protein is overexpressed in hyperproliferative skin diseases, exhibits antimicrobial activities against bacteria and induces immunomodulatory activities. [provided by RefSeq, Nov 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100A7	NM_002963.4	c.141+149A>T		intron_variant	Intron 2 of 2	ENST00000368723.4	NP_002954.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
S100A7	ENST00000368723.4	c.141+149A>T		intron_variant	Intron 2 of 2	1	NM_002963.4	ENSP00000357712.3
S100A7	ENST00000368722.5	c.141+149A>T		intron_variant	Intron 2 of 2	3		ENSP00000357711.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 674260 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 346852

African (AFR) AF: 0.00 AC: 0 AN: 16478

American (AMR) AF: 0.00 AC: 0 AN: 20810

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14924

East Asian (EAS) AF: 0.00 AC: 0 AN: 33750

South Asian (SAS) AF: 0.00 AC: 0 AN: 50786

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38698

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2410

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 463244

Other (OTH) AF: 0.00 AC: 0 AN: 33160

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.65
PhyloP100		-0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3014836; hg19: chr1-153431200;