rs8057939

Variant names:

• chr16-49360365-T-C
• rs8057939

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 0.17 in 152,082 control chromosomes in the GnomAD database, including 2,721 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 0.17 (2721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 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: 0.170 AC: 25877 AN: 151964 Hom.: 2712 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.170 AC: 25925 AN: 152082 Hom.: 2721 Cov.: 32 AF XY: 0.171 AC XY: 12751 AN XY: 74354

African (AFR) AF: 0.275 AC: 11396 AN: 41484

American (AMR) AF: 0.0991 AC: 1515 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1248 AN: 5140

South Asian (SAS) AF: 0.308 AC: 1480 AN: 4812

European-Finnish (FIN) AF: 0.121 AC: 1285 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8140 AN: 67976

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.132 Hom.: 7097

Bravo AF: 0.168

Asia WGS AF: 0.292 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.88
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8057939; hg19: chr16-49394276; COSMIC: COSV50192754;