rs197057

Variant names:

• chr16-1082015-C-G
• rs197057

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 0.519 in 151,982 control chromosomes in the GnomAD database, including 21,094 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 0.52 (21094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 5 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 (AMR) allele frequency at 95% confidence interval = 0.561 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: 0.519 AC: 78821 AN: 151864 Hom.: 21079 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.519 AC: 78878 AN: 151982 Hom.: 21094 Cov.: 32 AF XY: 0.518 AC XY: 38474 AN XY: 74272

African (AFR) AF: 0.524 AC: 21719 AN: 41436

American (AMR) AF: 0.571 AC: 8724 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3466

East Asian (EAS) AF: 0.131 AC: 673 AN: 5150

South Asian (SAS) AF: 0.326 AC: 1564 AN: 4798

European-Finnish (FIN) AF: 0.599 AC: 6334 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36889 AN: 67948

Other (OTH) AF: 0.498 AC: 1052 AN: 2114

Alfa AF: 0.538 Hom.: 2795

Bravo AF: 0.521

Asia WGS AF: 0.252 AC: 879 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	0.17
DANN	Benign	0.33
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs197057; hg19: chr16-1132015; COSMIC: COSV53513085;