6-32710135-C-T

Variant names:

• chr6-32710135-C-T
• rs9275563

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 0.437 in 151,206 control chromosomes in the GnomAD database, including 14,945 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 0.44 (14945 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 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: 0.437 AC: 65996 AN: 151092 Hom.: 14945 Cov.: 29

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.437 AC: 66026 AN: 151206 Hom.: 14945 Cov.: 29 AF XY: 0.433 AC XY: 31965 AN XY: 73876

African (AFR) AF: 0.373 AC: 15378 AN: 41180

American (AMR) AF: 0.522 AC: 7939 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2135 AN: 3454

East Asian (EAS) AF: 0.497 AC: 2552 AN: 5132

South Asian (SAS) AF: 0.535 AC: 2559 AN: 4784

European-Finnish (FIN) AF: 0.298 AC: 3122 AN: 10480

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30691 AN: 67684

Other (OTH) AF: 0.486 AC: 1014 AN: 2086

Alfa AF: 0.452 Hom.: 28992

Bravo AF: 0.455

Asia WGS AF: 0.538 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.2
DANN	Benign	0.48
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs9275563; hg19: chr6-32677912; COSMIC: COSV70582320;