chr16-56961126-T-C

Variant names:

• chr16-56961126-T-C
• rs4783962

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 0.786 in 445,188 control chromosomes in the GnomAD database, including 138,005 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 0.80 (48603 hom., cov: 33)
  • Exomes 𝑓: 0.78 (89402 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 15 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 (AFR) allele frequency at 95% confidence interval = 0.872 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: 0.797 AC: 121233 AN: 152134 Hom.: 48552 Cov.: 33

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.785

GnomAD4 exome AF: 0.780 AC: 228410 AN: 292936 Hom.: 89402 AF XY: 0.784 AC XY: 130369 AN XY: 166346

African (AFR) AF: 0.875 AC: 7368 AN: 8420

American (AMR) AF: 0.803 AC: 21413 AN: 26680

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 7310 AN: 9922

East Asian (EAS) AF: 0.648 AC: 5871 AN: 9058

South Asian (SAS) AF: 0.824 AC: 48196 AN: 58490

European-Finnish (FIN) AF: 0.726 AC: 8978 AN: 12366

Middle Eastern (MID) AF: 0.787 AC: 1692 AN: 2150

European-Non Finnish (NFE) AF: 0.769 AC: 116991 AN: 152192

Other (OTH) AF: 0.775 AC: 10591 AN: 13658

GnomAD4 genome AF: 0.797 AC: 121341 AN: 152252 Hom.: 48603 Cov.: 33 AF XY: 0.796 AC XY: 59268 AN XY: 74446

African (AFR) AF: 0.879 AC: 36556 AN: 41574

American (AMR) AF: 0.785 AC: 12011 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2570 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3407 AN: 5180

South Asian (SAS) AF: 0.827 AC: 3990 AN: 4822

European-Finnish (FIN) AF: 0.724 AC: 7663 AN: 10590

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52460 AN: 67992

Other (OTH) AF: 0.782 AC: 1654 AN: 2114

Alfa AF: 0.779 Hom.: 41249

Bravo AF: 0.804

Asia WGS AF: 0.745 AC: 2591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.76
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4783962; hg19: chr16-56995038;