rs2666138

Variant names:

• chr2-36104014-G-A
• rs2666138

Your query was ambiguous. Multiple possible variants found:

• chr2-36104014-G-A
• chr2-36104014-G-C
• chr2-36104014-G-T

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 0.861 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.873 AC: 36260 AN: 41532

American (AMR) AF: 0.881 AC: 13470 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3197 AN: 3468

East Asian (EAS) AF: 0.730 AC: 3770 AN: 5164

South Asian (SAS) AF: 0.761 AC: 3668 AN: 4818

European-Finnish (FIN) AF: 0.877 AC: 9302 AN: 10606

Middle Eastern (MID) AF: 0.880 AC: 257 AN: 292

European-Non Finnish (NFE) AF: 0.860 AC: 58465 AN: 68002

Other (OTH) AF: 0.869 AC: 1838 AN: 2116

Alfa AF: 0.862 Hom.: 249773

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2666138; hg19: chr2-36331157;