2-81242286-G-C

Variant names:

• chr2-81242286-G-C
• rs11126799

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 0.0564 in 150,610 control chromosomes in the GnomAD database, including 406 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 0.056 (406 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 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: 0.0564 AC: 8487 AN: 150496 Hom.: 407 Cov.: 29

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.0543

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

GnomAD4 genome AF: 0.0564 AC: 8489 AN: 150610 Hom.: 406 Cov.: 29 AF XY: 0.0596 AC XY: 4382 AN XY: 73534

Gnomad4 AFR AF: 0.0224

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0678

Gnomad4 NFE AF: 0.0563

Gnomad4 OTH AF: 0.0547

Alfa AF: 0.0177 Hom.: 19

Bravo AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.45

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;