3-117472145-G-A

Position:

• chr3-117472145-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 0.65 in 148,878 control chromosomes in the GnomAD database, including 32,680 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 0.65 (32680 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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: 0.650 AC: 96662 AN: 148754 Hom.: 32675 Cov.: 24

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.650 AC: 96705 AN: 148878 Hom.: 32680 Cov.: 24 AF XY: 0.655 AC XY: 47434 AN XY: 72462

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.666

Alfa AF: 0.681 Hom.: 4471

Bravo AF: 0.625

Asia WGS AF: 0.735 AC: 2538 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1910040; hg19: chr3-117190992;