rs952131

Variant names:

• chr11-129637139-G-T
• rs952131

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 0.168 in 152,182 control chromosomes in the GnomAD database, including 2,660 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 0.17 (2660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25523 AN: 152064 Hom.: 2658 Cov.: 32

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.168 AC: 25525 AN: 152182 Hom.: 2660 Cov.: 32 AF XY: 0.167 AC XY: 12416 AN XY: 74394

African (AFR) AF: 0.0543 AC: 2258 AN: 41550

American (AMR) AF: 0.189 AC: 2883 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1188 AN: 5176

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1939 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14845 AN: 67998

Other (OTH) AF: 0.188 AC: 395 AN: 2106

Alfa AF: 0.198 Hom.: 7104

Bravo AF: 0.164

Asia WGS AF: 0.218 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs952131; hg19: chr11-129507034;