chr2-81242286-G-A

Variant names:

• chr2-81242286-G-A
• rs11126799

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 0.0665 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.120 AC: 4912 AN: 41036

American (AMR) AF: 0.0411 AC: 620 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.0335 AC: 116 AN: 3466

East Asian (EAS) AF: 0.000392 AC: 2 AN: 5100

South Asian (SAS) AF: 0.0115 AC: 55 AN: 4770

European-Finnish (FIN) AF: 0.0521 AC: 538 AN: 10332

Middle Eastern (MID) AF: 0.0451 AC: 13 AN: 288

European-Non Finnish (NFE) AF: 0.0537 AC: 3628 AN: 67542

Other (OTH) AF: 0.0609 AC: 127 AN: 2084

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs11126799; hg19: chr2-81469410;