rs2000862

Variant names:

• chr11-134626565-A-G
• rs2000862

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 0.412 in 151,864 control chromosomes in the GnomAD database, including 13,014 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 0.41 (13014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62495 AN: 151748 Hom.: 12987 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.412 AC: 62565 AN: 151864 Hom.: 13014 Cov.: 32 AF XY: 0.405 AC XY: 30105 AN XY: 74246

African (AFR) AF: 0.444 AC: 18390 AN: 41378

American (AMR) AF: 0.343 AC: 5244 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1521 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1647 AN: 5172

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4816

European-Finnish (FIN) AF: 0.344 AC: 3611 AN: 10488

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29098 AN: 67938

Other (OTH) AF: 0.414 AC: 876 AN: 2114

Alfa AF: 0.421 Hom.: 22915

Bravo AF: 0.415

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.022
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2000862;

hg19: chr11-134496459;