chr16-53020498-A-G

Variant names:

• chr16-53020498-A-G
• rs8051957

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 0.637 in 151,520 control chromosomes in the GnomAD database, including 30,955 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 0.64 (30955 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 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: 0.637 AC: 96477 AN: 151402 Hom.: 30923 Cov.: 29

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.637 AC: 96564 AN: 151520 Hom.: 30955 Cov.: 29 AF XY: 0.633 AC XY: 46806 AN XY: 73966

African (AFR) AF: 0.611 AC: 25213 AN: 41252

American (AMR) AF: 0.657 AC: 9971 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2277 AN: 3468

East Asian (EAS) AF: 0.464 AC: 2385 AN: 5144

South Asian (SAS) AF: 0.608 AC: 2915 AN: 4792

European-Finnish (FIN) AF: 0.651 AC: 6817 AN: 10468

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44864 AN: 67922

Other (OTH) AF: 0.621 AC: 1300 AN: 2094

Alfa AF: 0.650 Hom.: 35958

Bravo AF: 0.635

Asia WGS AF: 0.560 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0020
DANN	Benign	0.35
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs8051957; hg19: chr16-53054410;