chr6-32245275-A-T

Variant names:

• chr6-32245275-A-T
• rs9267954

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 0.201 in 152,110 control chromosomes in the GnomAD database, including 3,456 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 0.20 (3456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 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: 0.201 AC: 30553 AN: 151992 Hom.: 3448 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.201 AC: 30561 AN: 152110 Hom.: 3456 Cov.: 33 AF XY: 0.199 AC XY: 14796 AN XY: 74342

African (AFR) AF: 0.114 AC: 4731 AN: 41494

American (AMR) AF: 0.265 AC: 4056 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3470

East Asian (EAS) AF: 0.132 AC: 682 AN: 5174

South Asian (SAS) AF: 0.189 AC: 909 AN: 4816

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10586

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16896 AN: 67972

Other (OTH) AF: 0.188 AC: 396 AN: 2106

Alfa AF: 0.111 Hom.: 181

Bravo AF: 0.205

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.89
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs9267954; hg19: chr6-32213052;