rs11126799

Positions:

• chr2-81242286-G-A
• chr2-81242286-G-C
• chr2-81242286-G-T

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 0.0665 in 150,610 control chromosomes in the GnomAD database, including 444 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 0.066 (444 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 9995 AN: 150498 Hom.: 444 Cov.: 29

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.0335

Gnomad EAS AF: 0.000391

Gnomad SAS AF: 0.0117

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0665 AC: 10013 AN: 150610 Hom.: 444 Cov.: 29 AF XY: 0.0641 AC XY: 4710 AN XY: 73524

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0335

Gnomad4 EAS AF: 0.000392

Gnomad4 SAS AF: 0.0115

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0537

Gnomad4 OTH AF: 0.0609

Alfa AF: 0.0272 Hom.: 19

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11126799; hg19: chr2-81469410;