6-25931349-A-G

Position:

• chr6-25931349-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 0.81 in 151,906 control chromosomes in the GnomAD database, including 50,276 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 0.81 (50276 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

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 (AFR) allele frequency at 95% confidence interval = 0.918 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: 0.810 AC: 122953 AN: 151788 Hom.: 50229 Cov.: 29

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.810 AC: 123052 AN: 151906 Hom.: 50276 Cov.: 29 AF XY: 0.808 AC XY: 60023 AN XY: 74246

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.808

Alfa AF: 0.767 Hom.: 89422

Bravo AF: 0.818

Asia WGS AF: 0.777 AC: 2704 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	3.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199741; hg19: chr6-25931577;