10-42845657-C-T

Variant names:

• chr10-42845657-C-T
• rs2142991

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 0.866 in 152,238 control chromosomes in the GnomAD database, including 57,181 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 0.87 (57181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 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: 0.866 AC: 131664 AN: 152120 Hom.: 57129 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.866 AC: 131775 AN: 152238 Hom.: 57181 Cov.: 32 AF XY: 0.866 AC XY: 64466 AN XY: 74436

African (AFR) AF: 0.927 AC: 38493 AN: 41544

American (AMR) AF: 0.847 AC: 12965 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3022 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4441 AN: 5172

South Asian (SAS) AF: 0.827 AC: 3993 AN: 4826

European-Finnish (FIN) AF: 0.863 AC: 9148 AN: 10600

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56757 AN: 68004

Other (OTH) AF: 0.866 AC: 1828 AN: 2112

Alfa AF: 0.846 Hom.: 183744

Bravo AF: 0.867

Asia WGS AF: 0.820 AC: 2855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.26
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2142991; hg19: chr10-43341105;