2-44099784-A-G

Variant names:

• chr2-44099784-A-G
• rs2333825

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 0.586 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
• 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 = 0.68 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

African (AFR) AF: 0.597 AC: 24697 AN: 41394

American (AMR) AF: 0.669 AC: 10221 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1578 AN: 3464

East Asian (EAS) AF: 0.699 AC: 3608 AN: 5160

South Asian (SAS) AF: 0.556 AC: 2681 AN: 4822

European-Finnish (FIN) AF: 0.598 AC: 6290 AN: 10526

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37976 AN: 67922

Other (OTH) AF: 0.569 AC: 1201 AN: 2112

Alfa AF: 0.560 Hom.: 70102

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2333825; hg19: chr2-44326923;