chr6-32133985-C-T

Variant names:

• chr6-32133985-C-T
• rs9267803

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 0.222 in 152,206 control chromosomes in the GnomAD database, including 4,882 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 0.22 (4882 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 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: 0.223 AC: 33852 AN: 152088 Hom.: 4879 Cov.: 33

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.222 AC: 33863 AN: 152206 Hom.: 4882 Cov.: 33 AF XY: 0.228 AC XY: 16966 AN XY: 74408

African (AFR) AF: 0.0520 AC: 2161 AN: 41556

American (AMR) AF: 0.289 AC: 4418 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1563 AN: 3466

East Asian (EAS) AF: 0.162 AC: 837 AN: 5174

South Asian (SAS) AF: 0.186 AC: 896 AN: 4828

European-Finnish (FIN) AF: 0.386 AC: 4079 AN: 10576

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18933 AN: 68006

Other (OTH) AF: 0.236 AC: 498 AN: 2112

Alfa AF: 0.256 Hom.: 13966

Bravo AF: 0.210

Asia WGS AF: 0.198 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.58
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9267803; hg19: chr6-32101762;