2-25170385-C-T

Variant names:

• chr2-25170385-C-T
• rs3754860

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 0.227 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0566 AC: 2350 AN: 41506

American (AMR) AF: 0.178 AC: 2725 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1486 AN: 5166

South Asian (SAS) AF: 0.334 AC: 1610 AN: 4814

European-Finnish (FIN) AF: 0.332 AC: 3516 AN: 10576

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21025 AN: 67952

Other (OTH) AF: 0.244 AC: 516 AN: 2114

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3754860; hg19: chr2-25393254;