chr16-50652646-A-C

Variant names:

• chr16-50652646-A-C
• rs7186163

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 0.626 in 152,140 control chromosomes in the GnomAD database, including 30,689 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 0.63 (30689 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95148 AN: 152022 Hom.: 30687 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.626 AC: 95176 AN: 152140 Hom.: 30689 Cov.: 33 AF XY: 0.625 AC XY: 46531 AN XY: 74392

African (AFR) AF: 0.500 AC: 20720 AN: 41458

American (AMR) AF: 0.565 AC: 8631 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2425 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2778 AN: 5184

South Asian (SAS) AF: 0.477 AC: 2302 AN: 4830

European-Finnish (FIN) AF: 0.766 AC: 8117 AN: 10590

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47967 AN: 68002

Other (OTH) AF: 0.627 AC: 1325 AN: 2114

Alfa AF: 0.664 Hom.: 8003

Bravo AF: 0.607

Asia WGS AF: 0.499 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.76
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7186163; hg19: chr16-50686557;