rs4783961

Variant names:

• chr16-56960982-G-A
• rs4783961

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 0.489 in 512,278 control chromosomes in the GnomAD database, including 62,567 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 0.47 (17289 hom., cov: 32)
  • Exomes 𝑓: 0.50 (45278 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71550 AN: 151934 Hom.: 17272 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.461

GnomAD2 exomes AF: 0.480 AC: 104286 AN: 217272 AF XY: 0.486

Gnomad AFR exome AF: 0.429

Gnomad AMR exome AF: 0.519

Gnomad ASJ exome AF: 0.484

Gnomad EAS exome AF: 0.227

Gnomad FIN exome AF: 0.444

Gnomad NFE exome AF: 0.499

Gnomad OTH exome AF: 0.481

GnomAD4 exome AF: 0.497 AC: 178942 AN: 360226 Hom.: 45278 Cov.: 0 AF XY: 0.502 AC XY: 103525 AN XY: 206362

African (AFR) AF: 0.424 AC: 4413 AN: 10404

American (AMR) AF: 0.520 AC: 18303 AN: 35224

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 5575 AN: 11586

East Asian (EAS) AF: 0.231 AC: 2992 AN: 12946

South Asian (SAS) AF: 0.560 AC: 36597 AN: 65370

European-Finnish (FIN) AF: 0.444 AC: 7313 AN: 16482

Middle Eastern (MID) AF: 0.445 AC: 1265 AN: 2844

European-Non Finnish (NFE) AF: 0.501 AC: 94585 AN: 188950

Other (OTH) AF: 0.481 AC: 7899 AN: 16420

GnomAD4 genome AF: 0.471 AC: 71604 AN: 152052 Hom.: 17289 Cov.: 32 AF XY: 0.469 AC XY: 34854 AN XY: 74334

African (AFR) AF: 0.434 AC: 17990 AN: 41490

American (AMR) AF: 0.486 AC: 7419 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1637 AN: 3464

East Asian (EAS) AF: 0.238 AC: 1231 AN: 5182

South Asian (SAS) AF: 0.560 AC: 2702 AN: 4826

European-Finnish (FIN) AF: 0.447 AC: 4730 AN: 10576

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34294 AN: 67930

Other (OTH) AF: 0.459 AC: 967 AN: 2108

Alfa AF: 0.488 Hom.: 46797

Bravo AF: 0.466

Asia WGS AF: 0.373 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4783961;

hg19: chr16-56994894;

COSMIC: COSV52363411;