2-114223390-G-T

Variant names:

• chr2-114223390-G-T
• rs3105491

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 0.606 in 151,488 control chromosomes in the GnomAD database, including 30,049 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 0.61 (30049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 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: 0.606 AC: 91770 AN: 151372 Hom.: 30040 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.606 AC: 91802 AN: 151488 Hom.: 30049 Cov.: 32 AF XY: 0.606 AC XY: 44903 AN XY: 74042

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.638

Alfa AF: 0.676 Hom.: 8762

Bravo AF: 0.595

Asia WGS AF: 0.654 AC: 2238 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3105491; hg19: chr2-114980967;