3-134473096-C-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 0.623 in 152,088 control chromosomes in the GnomAD database, including 30,340 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 0.62 (30340 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 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: 0.624 AC: 94807 AN: 151970 Hom.: 30351 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.623 AC: 94814 AN: 152088 Hom.: 30340 Cov.: 33 AF XY: 0.631 AC XY: 46917 AN XY: 74358

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.627

Alfa AF: 0.666 Hom.: 69258

Bravo AF: 0.610

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.7
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9841212; hg19: chr3-134191938;