chr6-129773253-C-T

Variant names:

• chr6-129773253-C-T
• rs2326864

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 0.135 in 152,160 control chromosomes in the GnomAD database, including 1,466 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 0.14 (1466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 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: 0.135 AC: 20502 AN: 152042 Hom.: 1457 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.135 AC: 20543 AN: 152160 Hom.: 1466 Cov.: 32 AF XY: 0.136 AC XY: 10126 AN XY: 74394

African (AFR) AF: 0.151 AC: 6260 AN: 41492

American (AMR) AF: 0.190 AC: 2910 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3468

East Asian (EAS) AF: 0.168 AC: 872 AN: 5184

South Asian (SAS) AF: 0.165 AC: 795 AN: 4818

European-Finnish (FIN) AF: 0.110 AC: 1167 AN: 10578

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7730 AN: 68014

Other (OTH) AF: 0.136 AC: 288 AN: 2116

Alfa AF: 0.125 Hom.: 683

Bravo AF: 0.142

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2326864; hg19: chr6-130094398;