2-186920086-C-T

Variant names:

• chr2-186920086-C-T
• rs2018302

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 0.75 in 151,648 control chromosomes in the GnomAD database, including 43,011 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 0.75 (43011 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• 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 (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.750 AC: 113602 AN: 151530 Hom.: 42976 Cov.: 30

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.750 AC: 113696 AN: 151648 Hom.: 43011 Cov.: 30 AF XY: 0.750 AC XY: 55531 AN XY: 74078

African (AFR) AF: 0.675 AC: 27822 AN: 41236

American (AMR) AF: 0.668 AC: 10181 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2614 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4241 AN: 5122

South Asian (SAS) AF: 0.659 AC: 3171 AN: 4814

European-Finnish (FIN) AF: 0.871 AC: 9161 AN: 10516

Middle Eastern (MID) AF: 0.670 AC: 193 AN: 288

European-Non Finnish (NFE) AF: 0.794 AC: 53966 AN: 67948

Other (OTH) AF: 0.751 AC: 1585 AN: 2110

Alfa AF: 0.724 Hom.: 4048

Bravo AF: 0.734

Asia WGS AF: 0.720 AC: 2506 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	0.36
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2018302; hg19: chr2-187784813;