6-32670217-T-C

Variant names:

• chr6-32670217-T-C
• rs9274741

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 0.53 in 148,930 control chromosomes in the GnomAD database, including 21,861 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 0.53 (21861 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.530 AC: 78836 AN: 148816 Hom.: 21848 Cov.: 30

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.530 AC: 78882 AN: 148930 Hom.: 21861 Cov.: 30 AF XY: 0.531 AC XY: 38614 AN XY: 72672

African (AFR) AF: 0.485 AC: 19845 AN: 40954

American (AMR) AF: 0.628 AC: 9333 AN: 14870

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2180 AN: 3368

East Asian (EAS) AF: 0.811 AC: 4120 AN: 5082

South Asian (SAS) AF: 0.668 AC: 3148 AN: 4710

European-Finnish (FIN) AF: 0.451 AC: 4636 AN: 10290

Middle Eastern (MID) AF: 0.695 AC: 196 AN: 282

European-Non Finnish (NFE) AF: 0.508 AC: 33774 AN: 66430

Other (OTH) AF: 0.561 AC: 1151 AN: 2050

Alfa AF: 0.527 Hom.: 34125

Bravo AF: 0.548

Asia WGS AF: 0.728 AC: 2527 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.40
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs9274741; hg19: chr6-32637994;