rs10185142

Variant names:

• chr2-237913689-C-T
• rs10185142

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 0.324 in 152,090 control chromosomes in the GnomAD database, including 8,317 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 0.32 (8317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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: 0.324 AC: 49304 AN: 151972 Hom.: 8307 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.324 AC: 49335 AN: 152090 Hom.: 8317 Cov.: 32 AF XY: 0.318 AC XY: 23609 AN XY: 74358

African (AFR) AF: 0.397 AC: 16460 AN: 41502

American (AMR) AF: 0.251 AC: 3830 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1075 AN: 5162

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4810

European-Finnish (FIN) AF: 0.265 AC: 2805 AN: 10574

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21395 AN: 67972

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.317 Hom.: 24899

Bravo AF: 0.326

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10185142; hg19: chr2-238822331;