6-131803662-C-G

Variant names:

• chr6-131803662-C-G
• rs11154643

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 0.092 in 152,060 control chromosomes in the GnomAD database, including 1,006 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 0.092 (1006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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: 0.0919 AC: 13961 AN: 151942 Hom.: 995 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0920 AC: 13995 AN: 152060 Hom.: 1006 Cov.: 32 AF XY: 0.0898 AC XY: 6679 AN XY: 74340

African (AFR) AF: 0.199 AC: 8224 AN: 41420

American (AMR) AF: 0.0732 AC: 1118 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3472

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5176

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4822

European-Finnish (FIN) AF: 0.0623 AC: 660 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3228 AN: 67984

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0242 Hom.: 17

Bravo AF: 0.0997

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11154643; hg19: chr6-132124802;