rs2000862

Variant names:

• chr11-134626565-A-G
• rs2000862

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.412 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

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.414

Alfa AF: 0.420 Hom.: 18033

Bravo AF: 0.415

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2000862; hg19: chr11-134496459;