2-240899087-G-T

Variant names:

• chr2-240899087-G-T
• rs4630763

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 0.513 in 152,114 control chromosomes in the GnomAD database, including 20,460 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 0.51 (20460 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.592 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: 0.513 AC: 78036 AN: 151994 Hom.: 20431 Cov.: 34

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.513 AC: 78105 AN: 152114 Hom.: 20460 Cov.: 34 AF XY: 0.510 AC XY: 37899 AN XY: 74342

African (AFR) AF: 0.598 AC: 24821 AN: 41508

American (AMR) AF: 0.363 AC: 5545 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1403 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2116 AN: 5172

South Asian (SAS) AF: 0.424 AC: 2041 AN: 4816

European-Finnish (FIN) AF: 0.537 AC: 5681 AN: 10572

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34965 AN: 67984

Other (OTH) AF: 0.465 AC: 983 AN: 2114

Alfa AF: 0.490 Hom.: 8267

Bravo AF: 0.527

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4630763; hg19: chr2-241838504;