chr6-32709311-C-T

Variant names:

• chr6-32709311-C-T
• rs9275555

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 0.24 in 150,180 control chromosomes in the GnomAD database, including 4,689 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 0.24 (4689 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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: 0.240 AC: 36055 AN: 150064 Hom.: 4683 Cov.: 27

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.240 AC: 36096 AN: 150180 Hom.: 4689 Cov.: 27 AF XY: 0.246 AC XY: 18067 AN XY: 73342

African (AFR) AF: 0.217 AC: 8875 AN: 40818

American (AMR) AF: 0.299 AC: 4514 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1049 AN: 3444

East Asian (EAS) AF: 0.306 AC: 1569 AN: 5124

South Asian (SAS) AF: 0.196 AC: 931 AN: 4738

European-Finnish (FIN) AF: 0.351 AC: 3618 AN: 10320

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14658 AN: 67354

Other (OTH) AF: 0.242 AC: 504 AN: 2082

Alfa AF: 0.243 Hom.: 8451

Bravo AF: 0.242

Asia WGS AF: 0.240 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs9275555; hg19: chr6-32677088;