6-82381359-A-T

Variant names:

• chr6-82381359-A-T
• rs9344274

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 0.38 in 151,910 control chromosomes in the GnomAD database, including 11,295 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 0.38 (11295 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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: 0.380 AC: 57663 AN: 151792 Hom.: 11278 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.380 AC: 57723 AN: 151910 Hom.: 11295 Cov.: 31 AF XY: 0.378 AC XY: 28034 AN XY: 74216

African (AFR) AF: 0.400 AC: 16582 AN: 41422

American (AMR) AF: 0.428 AC: 6524 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3117 AN: 5144

South Asian (SAS) AF: 0.460 AC: 2218 AN: 4826

European-Finnish (FIN) AF: 0.294 AC: 3101 AN: 10554

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.349 AC: 23682 AN: 67938

Other (OTH) AF: 0.341 AC: 717 AN: 2104

Alfa AF: 0.365 Hom.: 1289

Bravo AF: 0.387

Asia WGS AF: 0.528 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9344274; hg19: chr6-83091076;