chr2-48419260-T-C

Variant names:

• chr2-48419260-T-C
• rs10454142

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 0.225 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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0694 AC: 2883 AN: 41524

American (AMR) AF: 0.189 AC: 2883 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2385 AN: 5130

South Asian (SAS) AF: 0.171 AC: 822 AN: 4812

European-Finnish (FIN) AF: 0.366 AC: 3843 AN: 10496

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20111 AN: 67916

Other (OTH) AF: 0.220 AC: 464 AN: 2108

Alfa AF: 0.264 Hom.: 15172

Bravo AF: 0.207

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.54
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs10454142; hg19: chr2-48646399;