11-110525134-A-C

Variant names:

• chr11-110525134-A-C
• rs12785341

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 0.0795 in 152,250 control chromosomes in the GnomAD database, including 514 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 0.079 (514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 3 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 = 0.107 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: 0.0794 AC: 12083 AN: 152132 Hom.: 512 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0795 AC: 12098 AN: 152250 Hom.: 514 Cov.: 32 AF XY: 0.0765 AC XY: 5698 AN XY: 74442

African (AFR) AF: 0.110 AC: 4570 AN: 41528

American (AMR) AF: 0.0486 AC: 743 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3472

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5188

South Asian (SAS) AF: 0.0564 AC: 272 AN: 4824

European-Finnish (FIN) AF: 0.0563 AC: 598 AN: 10616

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5230 AN: 68010

Other (OTH) AF: 0.0658 AC: 139 AN: 2112

Alfa AF: 0.0745 Hom.: 1192

Bravo AF: 0.0791

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.93
DANN	Benign	0.33
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs12785341; hg19: chr11-110395858;