chr1-153543049-C-G

Variant names:

• chr1-153543049-C-G
• rs743687
• XM_017002029.2:c.22+191G>C

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+191G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,100 control chromosomes in the GnomAD database, including 1,619 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 0.12 (1619 hom., cov: 32)
• Consequence: S100A5 XM_017002029.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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: 0.116 AC: 17556 AN: 151982 Hom.: 1614 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.0531

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0556

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.116 AC: 17581 AN: 152100 Hom.: 1619 Cov.: 32 AF XY: 0.114 AC XY: 8479 AN XY: 74360

African (AFR) AF: 0.258 AC: 10707 AN: 41450

American (AMR) AF: 0.0870 AC: 1330 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3468

East Asian (EAS) AF: 0.0614 AC: 317 AN: 5164

South Asian (SAS) AF: 0.0792 AC: 381 AN: 4808

European-Finnish (FIN) AF: 0.0531 AC: 564 AN: 10614

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0556 AC: 3779 AN: 67994

Other (OTH) AF: 0.105 AC: 221 AN: 2104

Alfa AF: 0.0802 Hom.: 108

Bravo AF: 0.125

Asia WGS AF: 0.0940 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs743687; hg19: chr1-153515525;