rs2346747

Variant names:

• chr3-138135633-A-G
• rs2346747

Your query was ambiguous. Multiple possible variants found:

• chr3-138135633-A-G
• chr3-138135633-A-T

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 0.544 in 152,046 control chromosomes in the GnomAD database, including 25,003 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 0.54 (25003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.544 AC: 82640 AN: 151928 Hom.: 25002 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.544 AC: 82661 AN: 152046 Hom.: 25003 Cov.: 32 AF XY: 0.546 AC XY: 40595 AN XY: 74308

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.583

Alfa AF: 0.450 Hom.: 1347

Bravo AF: 0.532

Asia WGS AF: 0.534 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2346747; hg19: chr3-137854475;