6-32768326-T-C

Variant names:

• chr6-32768326-T-C
• rs9296043

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 0.502 in 151,950 control chromosomes in the GnomAD database, including 19,841 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 0.50 (19841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.502 AC: 76275 AN: 151830 Hom.: 19818 Cov.: 31

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.502 AC: 76350 AN: 151950 Hom.: 19841 Cov.: 31 AF XY: 0.512 AC XY: 38013 AN XY: 74236

African (AFR) AF: 0.543 AC: 22497 AN: 41418

American (AMR) AF: 0.506 AC: 7719 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3470

East Asian (EAS) AF: 0.762 AC: 3939 AN: 5170

South Asian (SAS) AF: 0.702 AC: 3380 AN: 4818

European-Finnish (FIN) AF: 0.538 AC: 5679 AN: 10546

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29379 AN: 67952

Other (OTH) AF: 0.527 AC: 1113 AN: 2110

Alfa AF: 0.457 Hom.: 32948

Bravo AF: 0.503

Asia WGS AF: 0.702 AC: 2431 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.5
DANN	Benign	0.53
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs9296043; hg19: chr6-32736103;