rs2488142

Positions:

• chr10-18050143-T-A

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 0.311 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.284

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2488142; hg19: chr10-18339072;