6-32703179-C-T

Variant names:

• chr6-32703179-C-T
• rs2856705

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 0.108 in 152,022 control chromosomes in the GnomAD database, including 1,086 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 0.11 (1086 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 41 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 (SAS) allele frequency at 95% confidence interval = 0.247 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: 0.108 AC: 16481 AN: 151904 Hom.: 1087 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.108 AC: 16478 AN: 152022 Hom.: 1086 Cov.: 33 AF XY: 0.108 AC XY: 8052 AN XY: 74342

African (AFR) AF: 0.111 AC: 4583 AN: 41454

American (AMR) AF: 0.105 AC: 1602 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 549 AN: 3462

East Asian (EAS) AF: 0.165 AC: 854 AN: 5176

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4810

European-Finnish (FIN) AF: 0.0394 AC: 417 AN: 10574

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.101 AC: 6859 AN: 67976

Other (OTH) AF: 0.134 AC: 282 AN: 2108

Alfa AF: 0.0994 Hom.: 1055

Bravo AF: 0.113

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.9
DANN	Benign	0.68
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs2856705; hg19: chr6-32670956;