rs11132508

Variant names:

• chr4-188064346-C-T
• rs11132508

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 0.651 in 151,436 control chromosomes in the GnomAD database, including 32,436 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 0.65 (32436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98453 AN: 151318 Hom.: 32406 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.651 AC: 98535 AN: 151436 Hom.: 32436 Cov.: 32 AF XY: 0.648 AC XY: 47957 AN XY: 73986

African (AFR) AF: 0.569 AC: 23482 AN: 41248

American (AMR) AF: 0.667 AC: 10149 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2689 AN: 3456

East Asian (EAS) AF: 0.894 AC: 4609 AN: 5154

South Asian (SAS) AF: 0.536 AC: 2573 AN: 4802

European-Finnish (FIN) AF: 0.621 AC: 6503 AN: 10466

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46294 AN: 67802

Other (OTH) AF: 0.682 AC: 1436 AN: 2106

Alfa AF: 0.679 Hom.: 28360

Bravo AF: 0.654

Asia WGS AF: 0.718 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	9.8
DANN	Benign	0.71
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11132508; hg19: chr4-188985500;