13-37557856-C-A

Variant names:

• chr13-37557856-C-A
• rs9547947

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 0.319 in 152,064 control chromosomes in the GnomAD database, including 8,537 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 0.32 (8537 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 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: 0.319 AC: 48519 AN: 151946 Hom.: 8535 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.319 AC: 48530 AN: 152064 Hom.: 8537 Cov.: 33 AF XY: 0.319 AC XY: 23710 AN XY: 74326

African (AFR) AF: 0.204 AC: 8459 AN: 41494

American (AMR) AF: 0.270 AC: 4131 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.0841 AC: 436 AN: 5182

South Asian (SAS) AF: 0.308 AC: 1488 AN: 4832

European-Finnish (FIN) AF: 0.434 AC: 4577 AN: 10552

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27150 AN: 67948

Other (OTH) AF: 0.327 AC: 690 AN: 2110

Alfa AF: 0.372 Hom.: 41744

Bravo AF: 0.302

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.20
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9547947; hg19: chr13-38131993;