chr6-32683340-T-G

Variant names:

• chr6-32683340-T-G
• rs9275141

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 0.503 in 147,072 control chromosomes in the GnomAD database, including 19,372 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 0.50 (19372 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 58 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 (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.503 AC: 73902 AN: 146960 Hom.: 19364 Cov.: 28

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.503 AC: 73942 AN: 147072 Hom.: 19372 Cov.: 28 AF XY: 0.504 AC XY: 36211 AN XY: 71796

African (AFR) AF: 0.461 AC: 18300 AN: 39714

American (AMR) AF: 0.610 AC: 9062 AN: 14850

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2149 AN: 3398

East Asian (EAS) AF: 0.768 AC: 3783 AN: 4926

South Asian (SAS) AF: 0.578 AC: 2671 AN: 4624

European-Finnish (FIN) AF: 0.437 AC: 4478 AN: 10244

Middle Eastern (MID) AF: 0.642 AC: 185 AN: 288

European-Non Finnish (NFE) AF: 0.480 AC: 31752 AN: 66118

Other (OTH) AF: 0.538 AC: 1093 AN: 2032

Alfa AF: 0.504 Hom.: 52845

Asia WGS AF: 0.664 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.57
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs9275141; hg19: chr6-32651117; COSMIC: COSV69193896;