chr6-32699045-C-T

Variant names:

• chr6-32699045-C-T
• rs9275328

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 0.163 in 151,926 control chromosomes in the GnomAD database, including 2,297 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 0.16 (2297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 24 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 = 0.274 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: 0.163 AC: 24781 AN: 151808 Hom.: 2289 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.163 AC: 24814 AN: 151926 Hom.: 2297 Cov.: 32 AF XY: 0.171 AC XY: 12698 AN XY: 74238

African (AFR) AF: 0.137 AC: 5671 AN: 41416

American (AMR) AF: 0.281 AC: 4298 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1292 AN: 5156

South Asian (SAS) AF: 0.119 AC: 575 AN: 4820

European-Finnish (FIN) AF: 0.258 AC: 2705 AN: 10500

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9087 AN: 67980

Other (OTH) AF: 0.150 AC: 317 AN: 2108

Alfa AF: 0.149 Hom.: 1437

Bravo AF: 0.170

Asia WGS AF: 0.174 AC: 608 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	3.8
DANN	Benign	0.44
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs9275328; hg19: chr6-32666822;