rs2666138

Positions:

• chr2-36104014-G-A
• chr2-36104014-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 0.861 in 152,196 control chromosomes in the GnomAD database, including 56,628 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 0.86 (56628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.869 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: 0.861 AC: 130952 AN: 152078 Hom.: 56556 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.861 AC: 131080 AN: 152196 Hom.: 56628 Cov.: 32 AF XY: 0.860 AC XY: 63974 AN XY: 74394

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.869

Alfa AF: 0.862 Hom.: 113446

Bravo AF: 0.865

Asia WGS AF: 0.782 AC: 2718 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2666138; hg19: chr2-36331157;