chr3-38650537-A-G

Variant names:

• chr3-38650537-A-G
• rs41310239

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 0.121 in 151,858 control chromosomes in the GnomAD database, including 1,386 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 0.12 (1386 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 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: 0.121 AC: 18418 AN: 151740 Hom.: 1385 Cov.: 31

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0850

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.121 AC: 18426 AN: 151858 Hom.: 1386 Cov.: 31 AF XY: 0.119 AC XY: 8837 AN XY: 74184

African (AFR) AF: 0.0364 AC: 1507 AN: 41416

American (AMR) AF: 0.123 AC: 1881 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.0846 AC: 431 AN: 5096

South Asian (SAS) AF: 0.198 AC: 952 AN: 4802

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11251 AN: 67928

Other (OTH) AF: 0.137 AC: 289 AN: 2108

Alfa AF: 0.131 Hom.: 196

Bravo AF: 0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.16
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs41310239; hg19: chr3-38692028;