rs10454142

Variant names:

• chr2-48419260-T-C
• rs10454142

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 0.225 in 151,950 control chromosomes in the GnomAD database, including 4,810 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 (4810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.225 AC: 34182 AN: 151832 Hom.: 4812 Cov.: 32

Gnomad AFR AF: 0.0694

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.225 AC: 34190 AN: 151950 Hom.: 4810 Cov.: 32 AF XY: 0.227 AC XY: 16820 AN XY: 74238

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.220

Alfa AF: 0.279 Hom.: 9328

Bravo AF: 0.207

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10454142; hg19: chr2-48646399;