6-147986782-A-G

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 0.928 in 152,218 control chromosomes in the GnomAD database, including 65,633 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 0.93 (65633 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 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: 0.928 AC: 141111 AN: 152100 Hom.: 65577 Cov.: 32

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.928 AC: 141224 AN: 152218 Hom.: 65633 Cov.: 32 AF XY: 0.926 AC XY: 68904 AN XY: 74416

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.921

Alfa AF: 0.932 Hom.: 86888

Bravo AF: 0.916

Asia WGS AF: 0.911 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.27
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6570808; hg19: chr6-148307918;