chr11-13211191-G-A

Variant names:

• chr11-13211191-G-A
• rs2170436

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 0.606 in 152,004 control chromosomes in the GnomAD database, including 30,106 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 0.61 (30106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92169 AN: 151886 Hom.: 30107 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.606 AC: 92183 AN: 152004 Hom.: 30106 Cov.: 32 AF XY: 0.609 AC XY: 45244 AN XY: 74292

African (AFR) AF: 0.357 AC: 14802 AN: 41446

American (AMR) AF: 0.610 AC: 9304 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2201 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4255 AN: 5174

South Asian (SAS) AF: 0.740 AC: 3557 AN: 4810

European-Finnish (FIN) AF: 0.681 AC: 7195 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48842 AN: 67972

Other (OTH) AF: 0.610 AC: 1290 AN: 2114

Alfa AF: 0.689 Hom.: 57695

Bravo AF: 0.586

Asia WGS AF: 0.745 AC: 2580 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.3
DANN	Benign	0.14
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2170436; hg19: chr11-13232738;