rs9302752

Variant names:

• chr16-50685192-T-C
• rs9302752

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 0.674 in 152,034 control chromosomes in the GnomAD database, including 35,568 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 0.67 (35568 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 79 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102363 AN: 151916 Hom.: 35551 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.674 AC: 102427 AN: 152034 Hom.: 35568 Cov.: 31 AF XY: 0.666 AC XY: 49459 AN XY: 74292

African (AFR) AF: 0.647 AC: 26790 AN: 41428

American (AMR) AF: 0.617 AC: 9428 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2851 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1308 AN: 5172

South Asian (SAS) AF: 0.366 AC: 1764 AN: 4824

European-Finnish (FIN) AF: 0.724 AC: 7644 AN: 10560

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.740 AC: 50339 AN: 67982

Other (OTH) AF: 0.671 AC: 1415 AN: 2110

Alfa AF: 0.713 Hom.: 118067

Bravo AF: 0.665

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.30
DANN	Benign	0.57
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs9302752; hg19: chr16-50719103;