chr10-42923545-T-C

Variant names:

• chr10-42923545-T-C
• rs2488291

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 0.123 in 152,238 control chromosomes in the GnomAD database, including 1,421 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 0.12 (1421 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18776 AN: 152120 Hom.: 1423 Cov.: 36

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.0922

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.123 AC: 18759 AN: 152238 Hom.: 1421 Cov.: 36 AF XY: 0.127 AC XY: 9480 AN XY: 74422

African (AFR) AF: 0.0715 AC: 2970 AN: 41560

American (AMR) AF: 0.190 AC: 2904 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.269 AC: 1396 AN: 5184

South Asian (SAS) AF: 0.252 AC: 1217 AN: 4824

European-Finnish (FIN) AF: 0.0922 AC: 977 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8132 AN: 68000

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.123 Hom.: 174

Bravo AF: 0.125

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.63
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs2488291; hg19: chr10-43418993;