11-13596061-A-G

Variant names:

• chr11-13596061-A-G
• rs2036417

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 0.545 in 151,928 control chromosomes in the GnomAD database, including 23,599 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 0.54 (23599 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.619 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: 0.545 AC: 82697 AN: 151808 Hom.: 23594 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.545 AC: 82730 AN: 151928 Hom.: 23599 Cov.: 31 AF XY: 0.549 AC XY: 40747 AN XY: 74224

African (AFR) AF: 0.359 AC: 14858 AN: 41432

American (AMR) AF: 0.580 AC: 8857 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2428 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2780 AN: 5154

South Asian (SAS) AF: 0.638 AC: 3061 AN: 4796

European-Finnish (FIN) AF: 0.625 AC: 6589 AN: 10542

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42268 AN: 67948

Other (OTH) AF: 0.556 AC: 1174 AN: 2110

Alfa AF: 0.591 Hom.: 74441

Bravo AF: 0.527

Asia WGS AF: 0.578 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.43
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs2036417; hg19: chr11-13617608;