1-153460264-T-C

Variant names:

• chr1-153460264-T-C
• rs3014839
• NM_002963.4:c.-18+344A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002963.4(S100A7):​c.-18+344A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 152,254 control chromosomes in the GnomAD database, including 57,261 homozygotes. 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: 𝑓 0.86 (57261 hom., cov: 33)
• Consequence: S100A7 NM_002963.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100A7	NM_002963.4	c.-18+344A>G		intron_variant	Intron 1 of 2	ENST00000368723.4	NP_002954.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
S100A7	ENST00000368723.4	c.-18+344A>G		intron_variant	Intron 1 of 2	1	NM_002963.4	ENSP00000357712.3

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131518 AN: 152136 Hom.: 57188 Cov.: 33

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.847

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.865 AC: 131652 AN: 152254 Hom.: 57261 Cov.: 33 AF XY: 0.863 AC XY: 64278 AN XY: 74440

African (AFR) AF: 0.945 AC: 39267 AN: 41568

American (AMR) AF: 0.842 AC: 12891 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2877 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3829 AN: 5152

South Asian (SAS) AF: 0.702 AC: 3391 AN: 4828

European-Finnish (FIN) AF: 0.911 AC: 9667 AN: 10614

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56941 AN: 68004

Other (OTH) AF: 0.848 AC: 1792 AN: 2112

Alfa AF: 0.856 Hom.: 9357

Bravo AF: 0.864

Asia WGS AF: 0.751 AC: 2614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.078
DANN	Benign	0.34
PhyloP100		-3.2
PromoterAI		-0.0043	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3014839; hg19: chr1-153432740;