chr16-53003763-A-G

Variant names:

• chr16-53003763-A-G
• rs1990637

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 0.628 in 152,082 control chromosomes in the GnomAD database, including 31,922 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 (31922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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: 0.629 AC: 95547 AN: 151964 Hom.: 31914 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.628 AC: 95574 AN: 152082 Hom.: 31922 Cov.: 32 AF XY: 0.634 AC XY: 47164 AN XY: 74340

African (AFR) AF: 0.388 AC: 16114 AN: 41488

American (AMR) AF: 0.697 AC: 10650 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3472

East Asian (EAS) AF: 0.931 AC: 4814 AN: 5170

South Asian (SAS) AF: 0.682 AC: 3278 AN: 4806

European-Finnish (FIN) AF: 0.771 AC: 8153 AN: 10574

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48234 AN: 67984

Other (OTH) AF: 0.631 AC: 1334 AN: 2114

Alfa AF: 0.638 Hom.: 4865

Bravo AF: 0.615

Asia WGS AF: 0.727 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.9
DANN	Benign	0.91
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1990637; hg19: chr16-53037675;