chr3-38651526-G-A

Variant names:

• chr3-38651526-G-A
• rs41310749

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 0.15 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.138 AC: 5718 AN: 41286

American (AMR) AF: 0.135 AC: 2053 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3470

East Asian (EAS) AF: 0.0641 AC: 325 AN: 5068

South Asian (SAS) AF: 0.197 AC: 946 AN: 4794

European-Finnish (FIN) AF: 0.138 AC: 1448 AN: 10494

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11272 AN: 67898

Other (OTH) AF: 0.151 AC: 317 AN: 2102

Alfa AF: 0.159 Hom.: 2899

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs41310749; hg19: chr3-38693017;