2-25190440-C-T

Variant names:

• chr2-25190440-C-T
• rs4665287

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 0.18 in 152,188 control chromosomes in the GnomAD database, including 2,965 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 0.18 (2965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 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: 0.180 AC: 27387 AN: 152070 Hom.: 2950 Cov.: 32

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.180 AC: 27420 AN: 152188 Hom.: 2965 Cov.: 32 AF XY: 0.189 AC XY: 14049 AN XY: 74396

Gnomad4 AFR AF: 0.0977

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.182

Alfa AF: 0.184 Hom.: 1629

Bravo AF: 0.183

Asia WGS AF: 0.188 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4665287; hg19: chr2-25413309;