rs2147556

Variant names:

• chr13-72538333-A-G
• rs2147556

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.660

Alfa AF: 0.698 Hom.: 48833

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

Splicing

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

Publications

LitVar

Other links and lift over

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