6-32701379-T-C

Variant names:

• chr6-32701379-T-C
• rs9275390

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 0.295 in 151,900 control chromosomes in the GnomAD database, including 7,031 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 0.29 (7031 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 62 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 (AMR) allele frequency at 95% confidence interval = 0.389 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: 0.294 AC: 44686 AN: 151782 Hom.: 7015 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.295 AC: 44747 AN: 151900 Hom.: 7031 Cov.: 31 AF XY: 0.304 AC XY: 22585 AN XY: 74226

African (AFR) AF: 0.293 AC: 12149 AN: 41400

American (AMR) AF: 0.397 AC: 6064 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3472

East Asian (EAS) AF: 0.296 AC: 1526 AN: 5162

South Asian (SAS) AF: 0.211 AC: 1018 AN: 4818

European-Finnish (FIN) AF: 0.465 AC: 4882 AN: 10490

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16948 AN: 67968

Other (OTH) AF: 0.288 AC: 608 AN: 2110

Alfa AF: 0.273 Hom.: 19379

Bravo AF: 0.295

Asia WGS AF: 0.275 AC: 959 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.34
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs9275390; hg19: chr6-32669156;