6-91940517-T-G

Position:

• chr6-91940517-T-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 0.746 in 151,894 control chromosomes in the GnomAD database, including 42,521 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 0.75 (42521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.81 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: 0.745 AC: 113130 AN: 151776 Hom.: 42461 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.746 AC: 113246 AN: 151894 Hom.: 42521 Cov.: 32 AF XY: 0.746 AC XY: 55388 AN XY: 74228

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.746

Alfa AF: 0.713 Hom.: 57335

Bravo AF: 0.761

Asia WGS AF: 0.780 AC: 2709 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.077
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1498252; hg19: chr6-92650235;