10-42845657-C-T

Position:

• chr10-42845657-C-T

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 0.866 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.42845657C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.866

Alfa AF: 0.841 Hom.: 78315

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2142991; hg19: chr10-43341105;