rs2488142

Variant names:

• chr10-18050143-T-A
• rs2488142

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 0.311 in 151,972 control chromosomes in the GnomAD database, including 8,081 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 0.31 (8081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.311 AC: 47191 AN: 151854 Hom.: 8075 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.311 AC: 47229 AN: 151972 Hom.: 8081 Cov.: 32 AF XY: 0.312 AC XY: 23153 AN XY: 74270

African (AFR) AF: 0.454 AC: 18815 AN: 41414

American (AMR) AF: 0.268 AC: 4087 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1821 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2946 AN: 10578

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16762 AN: 67970

Other (OTH) AF: 0.284 AC: 599 AN: 2112

Alfa AF: 0.290 Hom.: 880

Bravo AF: 0.318

Asia WGS AF: 0.289 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.20
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2488142; hg19: chr10-18339072;