chr11-131140898-T-C

Variant names:

• chr11-131140898-T-C
• rs1627835

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 0.767 in 152,186 control chromosomes in the GnomAD database, including 45,042 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 0.77 (45042 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 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: 0.766 AC: 116556 AN: 152068 Hom.: 44993 Cov.: 33

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.767 AC: 116671 AN: 152186 Hom.: 45042 Cov.: 33 AF XY: 0.768 AC XY: 57137 AN XY: 74386

African (AFR) AF: 0.858 AC: 35643 AN: 41538

American (AMR) AF: 0.745 AC: 11392 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2634 AN: 3470

East Asian (EAS) AF: 0.876 AC: 4516 AN: 5158

South Asian (SAS) AF: 0.796 AC: 3843 AN: 4828

European-Finnish (FIN) AF: 0.762 AC: 8071 AN: 10592

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48069 AN: 67984

Other (OTH) AF: 0.750 AC: 1583 AN: 2110

Alfa AF: 0.724 Hom.: 116970

Bravo AF: 0.767

Asia WGS AF: 0.848 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1627835; hg19: chr11-131010793;