rs2147556

Variant names:

• chr13-72538333-A-G
• rs2147556

Variant summary

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

The variant allele was found at a frequency of 0.676 in 151,978 control chromosomes in the GnomAD database, including 35,006 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 0.68 (35006 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102658 AN: 151862 Hom.: 34972 Cov.: 30

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.676 AC: 102753 AN: 151978 Hom.: 35006 Cov.: 30 AF XY: 0.670 AC XY: 49756 AN XY: 74250

African (AFR) AF: 0.683 AC: 28309 AN: 41444

American (AMR) AF: 0.638 AC: 9755 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2396 AN: 3464

East Asian (EAS) AF: 0.446 AC: 2295 AN: 5140

South Asian (SAS) AF: 0.647 AC: 3114 AN: 4812

European-Finnish (FIN) AF: 0.622 AC: 6561 AN: 10552

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48145 AN: 67976

Other (OTH) AF: 0.660 AC: 1391 AN: 2106

Alfa AF: 0.696 Hom.: 61919

Bravo AF: 0.674

Asia WGS AF: 0.555 AC: 1929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2147556; hg19: chr13-73112471; COSMIC: COSV69363423;