chr6-32753194-C-T

Variant names:

• chr6-32753194-C-T
• rs9276529

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 0.12 in 151,932 control chromosomes in the GnomAD database, including 1,778 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 0.12 (1778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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: 0.120 AC: 18183 AN: 151814 Hom.: 1778 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0154

Gnomad FIN AF: 0.00531

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.120 AC: 18186 AN: 151932 Hom.: 1778 Cov.: 32 AF XY: 0.115 AC XY: 8555 AN XY: 74232

African (AFR) AF: 0.261 AC: 10802 AN: 41386

American (AMR) AF: 0.131 AC: 1995 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0783 AC: 272 AN: 3472

East Asian (EAS) AF: 0.00541 AC: 28 AN: 5180

South Asian (SAS) AF: 0.0154 AC: 74 AN: 4806

European-Finnish (FIN) AF: 0.00531 AC: 56 AN: 10548

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0676 AC: 4595 AN: 67966

Other (OTH) AF: 0.148 AC: 312 AN: 2104

Alfa AF: 0.0809 Hom.: 433

Bravo AF: 0.140

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.22
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9276529; hg19: chr6-32720971; COSMIC: COSV68616080;