2-240369088-G-A

Variant names:

• chr2-240369088-G-A
• rs1574192

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 0.263 in 152,114 control chromosomes in the GnomAD database, including 6,600 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 0.26 (6600 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39999 AN: 151996 Hom.: 6603 Cov.: 33

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.263 AC: 39993 AN: 152114 Hom.: 6600 Cov.: 33 AF XY: 0.258 AC XY: 19167 AN XY: 74350

African (AFR) AF: 0.0947 AC: 3932 AN: 41512

American (AMR) AF: 0.243 AC: 3710 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3472

East Asian (EAS) AF: 0.0163 AC: 84 AN: 5162

South Asian (SAS) AF: 0.154 AC: 745 AN: 4828

European-Finnish (FIN) AF: 0.350 AC: 3705 AN: 10572

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25899 AN: 67968

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.321 Hom.: 18030

Bravo AF: 0.246

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1574192; hg19: chr2-241308505;