rs950146

Variant names:

• chr3-36638607-G-T
• rs950146

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 0.488 in 152,050 control chromosomes in the GnomAD database, including 18,364 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 0.49 (18364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 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: 0.488 AC: 74146 AN: 151932 Hom.: 18358 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.488 AC: 74180 AN: 152050 Hom.: 18364 Cov.: 32 AF XY: 0.487 AC XY: 36194 AN XY: 74294

African (AFR) AF: 0.420 AC: 17432 AN: 41464

American (AMR) AF: 0.553 AC: 8453 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2501 AN: 5148

South Asian (SAS) AF: 0.428 AC: 2065 AN: 4822

European-Finnish (FIN) AF: 0.495 AC: 5227 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35238 AN: 67982

Other (OTH) AF: 0.503 AC: 1062 AN: 2110

Alfa AF: 0.503 Hom.: 43120

Bravo AF: 0.494

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.51
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs950146; hg19: chr3-36680099;