16-52916152-G-A

Variant names:

• chr16-52916152-G-A
• rs11645369

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 0.713 in 152,082 control chromosomes in the GnomAD database, including 39,378 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 0.71 (39378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.713 AC: 108336 AN: 151964 Hom.: 39374 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.713 AC: 108379 AN: 152082 Hom.: 39378 Cov.: 32 AF XY: 0.716 AC XY: 53249 AN XY: 74356

African (AFR) AF: 0.562 AC: 23272 AN: 41436

American (AMR) AF: 0.737 AC: 11266 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2674 AN: 3468

East Asian (EAS) AF: 0.934 AC: 4828 AN: 5170

South Asian (SAS) AF: 0.790 AC: 3811 AN: 4824

European-Finnish (FIN) AF: 0.801 AC: 8490 AN: 10602

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51574 AN: 67984

Other (OTH) AF: 0.743 AC: 1570 AN: 2112

Alfa AF: 0.747 Hom.: 22668

Bravo AF: 0.701

Asia WGS AF: 0.822 AC: 2859 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	0.23
DANN	Benign	0.74
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs11645369; hg19: chr16-52950064;