6-25931349-A-G

Variant names:

• chr6-25931349-A-G
• rs199741

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;