rs41310749

chr3-38651526-G-Achr3-38651526-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.15 in 151,566 control chromosomes in the GnomAD database, including 1,788 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 0.15 (1788 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22718 AN: 151448 Hom.: 1788 Cov.: 30

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.150 AC: 22743 AN: 151566 Hom.: 1788 Cov.: 30 AF XY: 0.147 AC XY: 10877 AN XY: 74048

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0641

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.151

Alfa AF: 0.145 Hom.: 252

Bravo AF: 0.149

Asia WGS AF: 0.134 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.8
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41310749; hg19: chr3-38693017;