2-117705629-A-T

Variant names:

• chr2-117705629-A-T
• rs2194494

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 0.833 in 152,240 control chromosomes in the GnomAD database, including 53,397 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 0.83 (53397 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 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: 0.833 AC: 126741 AN: 152122 Hom.: 53368 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.833 AC: 126820 AN: 152240 Hom.: 53397 Cov.: 33 AF XY: 0.835 AC XY: 62191 AN XY: 74442

African (AFR) AF: 0.697 AC: 28957 AN: 41516

American (AMR) AF: 0.908 AC: 13889 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3203 AN: 3472

East Asian (EAS) AF: 0.967 AC: 5007 AN: 5180

South Asian (SAS) AF: 0.901 AC: 4346 AN: 4826

European-Finnish (FIN) AF: 0.875 AC: 9277 AN: 10608

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59239 AN: 68024

Other (OTH) AF: 0.882 AC: 1862 AN: 2110

Alfa AF: 0.841 Hom.: 6766

Bravo AF: 0.830

Asia WGS AF: 0.920 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.73
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2194494; hg19: chr2-118463205;