rs6439167

chr3-129331913-T-C

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 0.816 in 152,190 control chromosomes in the GnomAD database, including 50,826 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 0.82 (50826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.816 AC: 124074 AN: 152072 Hom.: 50799 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.816 AC: 124159 AN: 152190 Hom.: 50826 Cov.: 32 AF XY: 0.817 AC XY: 60762 AN XY: 74410

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.806

Alfa AF: 0.796 Hom.: 60970

Bravo AF: 0.815

Asia WGS AF: 0.844 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.2
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6439167; hg19: chr3-129050756;