6-91940517-T-G

Variant names:

• chr6-91940517-T-G
• rs1498252

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.807 AC: 33442 AN: 41464

American (AMR) AF: 0.822 AC: 12524 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2875 AN: 3468

East Asian (EAS) AF: 0.686 AC: 3514 AN: 5126

South Asian (SAS) AF: 0.803 AC: 3857 AN: 4806

European-Finnish (FIN) AF: 0.649 AC: 6840 AN: 10546

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47637 AN: 67924

Other (OTH) AF: 0.746 AC: 1576 AN: 2112

Alfa AF: 0.714 Hom.: 82574

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1498252; hg19: chr6-92650235;