rs11177131

Variant names:

• chr12-68243668-C-T
• rs11177131

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 0.129 in 152,072 control chromosomes in the GnomAD database, including 1,546 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 0.13 (1546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 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: 0.129 AC: 19661 AN: 151954 Hom.: 1550 Cov.: 32

Gnomad AFR AF: 0.0579

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0980

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.129 AC: 19649 AN: 152072 Hom.: 1546 Cov.: 32 AF XY: 0.136 AC XY: 10098 AN XY: 74332

African (AFR) AF: 0.0579 AC: 2404 AN: 41492

American (AMR) AF: 0.137 AC: 2090 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3468

East Asian (EAS) AF: 0.0975 AC: 504 AN: 5170

South Asian (SAS) AF: 0.106 AC: 508 AN: 4814

European-Finnish (FIN) AF: 0.290 AC: 3058 AN: 10552

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9726 AN: 67982

Other (OTH) AF: 0.147 AC: 311 AN: 2110

Alfa AF: 0.130 Hom.: 484

Bravo AF: 0.120

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.61
DANN	Benign	0.74
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs11177131; hg19: chr12-68637448;