2-44099784-A-G

Variant names:

• chr2-44099784-A-G
• rs2333825

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 0.586 in 151,880 control chromosomes in the GnomAD database, including 26,144 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 0.59 (26144 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -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 = 0.68 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: 0.586 AC: 88901 AN: 151758 Hom.: 26130 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.586 AC: 88955 AN: 151880 Hom.: 26144 Cov.: 31 AF XY: 0.589 AC XY: 43676 AN XY: 74196

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.569

Alfa AF: 0.557 Hom.: 47600

Bravo AF: 0.593

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2333825; hg19: chr2-44326923;