2-25170385-C-T

Variant names:

• chr2-25170385-C-T
• rs3754860

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 0.227 in 152,076 control chromosomes in the GnomAD database, including 4,813 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 0.23 (4813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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: 0.227 AC: 34539 AN: 151958 Hom.: 4815 Cov.: 32

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.227 AC: 34526 AN: 152076 Hom.: 4813 Cov.: 32 AF XY: 0.227 AC XY: 16914 AN XY: 74350

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.244

Alfa AF: 0.251 Hom.: 702

Bravo AF: 0.206

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.27
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754860; hg19: chr2-25393254;