chr16-50952397-G-A

Variant names:

• chr16-50952397-G-A
• rs1564981

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 0.6 in 152,100 control chromosomes in the GnomAD database, including 29,888 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 0.60 (29888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 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: 0.600 AC: 91139 AN: 151982 Hom.: 29831 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.600 AC: 91252 AN: 152100 Hom.: 29888 Cov.: 32 AF XY: 0.604 AC XY: 44868 AN XY: 74328

African (AFR) AF: 0.862 AC: 35780 AN: 41524

American (AMR) AF: 0.602 AC: 9204 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2244 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3565 AN: 5150

South Asian (SAS) AF: 0.741 AC: 3570 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4395 AN: 10578

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30739 AN: 67956

Other (OTH) AF: 0.598 AC: 1263 AN: 2112

Alfa AF: 0.504 Hom.: 75042

Bravo AF: 0.625

Asia WGS AF: 0.726 AC: 2527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.23
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1564981; hg19: chr16-50986308;