6-117284828-T-C

Variant names:

• chr6-117284828-T-C
• rs13201929

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 0.0945 in 151,960 control chromosomes in the GnomAD database, including 871 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 0.094 (871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 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: 0.0945 AC: 14351 AN: 151842 Hom.: 872 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0930

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

GnomAD4 genome AF: 0.0945 AC: 14355 AN: 151960 Hom.: 871 Cov.: 32 AF XY: 0.0933 AC XY: 6929 AN XY: 74262

African (AFR) AF: 0.0248 AC: 1028 AN: 41428

American (AMR) AF: 0.0827 AC: 1261 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3464

East Asian (EAS) AF: 0.180 AC: 931 AN: 5168

South Asian (SAS) AF: 0.112 AC: 537 AN: 4816

European-Finnish (FIN) AF: 0.101 AC: 1065 AN: 10568

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8715 AN: 67946

Other (OTH) AF: 0.0935 AC: 197 AN: 2108

Alfa AF: 0.110 Hom.: 2579

Bravo AF: 0.0920

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs13201929; hg19: chr6-117605991;