6-26065393-A-G

Position:

• chr6-26065393-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 0.756 in 152,050 control chromosomes in the GnomAD database, including 44,298 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 0.76 (44298 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 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: 0.756 AC: 114831 AN: 151932 Hom.: 44255 Cov.: 30

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.756 AC: 114930 AN: 152050 Hom.: 44298 Cov.: 30 AF XY: 0.754 AC XY: 56061 AN XY: 74312

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.775

Alfa AF: 0.712 Hom.: 13610

Bravo AF: 0.769

Asia WGS AF: 0.739 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.54
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807212; hg19: chr6-26065621;