1-153542644-T-C

Variant names:

• chr1-153542644-T-C
• rs1810765
• XM_017002029.2:c.22+596A>G

Variant summary

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

The XM_017002029.2(S100A5):​c.22+596A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,054 control chromosomes in the GnomAD database, including 7,895 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 0.21 (7895 hom., cov: 32)
• Consequence: S100A5 XM_017002029.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 2 publications found

Genes affected

S100A5 (HGNC:10495): (S100 calcium binding protein A5) 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 has a Ca2+ affinity 20- to 100-fold higher than the other S100 proteins studied under identical conditions. This protein also binds Zn2+ and Cu2+, and Cu2+ strongly which impairs the binding of Ca2+. This protein is expressed in very restricted regions of the adult brain. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32505 AN: 151936 Hom.: 7859 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0638

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.214 AC: 32596 AN: 152054 Hom.: 7895 Cov.: 32 AF XY: 0.208 AC XY: 15500 AN XY: 74360

African (AFR) AF: 0.600 AC: 24828 AN: 41378

American (AMR) AF: 0.126 AC: 1934 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3470

East Asian (EAS) AF: 0.0632 AC: 327 AN: 5174

South Asian (SAS) AF: 0.0823 AC: 397 AN: 4826

European-Finnish (FIN) AF: 0.0533 AC: 566 AN: 10610

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0564 AC: 3834 AN: 67986

Other (OTH) AF: 0.180 AC: 381 AN: 2112

Alfa AF: 0.128 Hom.: 2071

Bravo AF: 0.237

Asia WGS AF: 0.130 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.57
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1810765; hg19: chr1-153515120;