3-115729685-G-A

Position:

• chr3-115729685-G-A

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 0.481 in 151,946 control chromosomes in the GnomAD database, including 18,724 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 0.48 (18724 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73041 AN: 151828 Hom.: 18688 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.481 AC: 73123 AN: 151946 Hom.: 18724 Cov.: 31 AF XY: 0.481 AC XY: 35735 AN XY: 74270

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.470

Alfa AF: 0.440 Hom.: 2580

Bravo AF: 0.490

Asia WGS AF: 0.323 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2918206; hg19: chr3-115448532;