chr2-117705629-A-T

Variant names:

• chr2-117705629-A-T
• rs2194494

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 0.833 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.967

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.882

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2194494; hg19: chr2-118463205;