10-42942522-T-C

Position:

• chr10-42942522-T-C

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 0.365 in 152,042 control chromosomes in the GnomAD database, including 11,520 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 0.37 (11520 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.365 AC: 55523 AN: 151924 Hom.: 11518 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.365 AC: 55533 AN: 152042 Hom.: 11520 Cov.: 33 AF XY: 0.374 AC XY: 27824 AN XY: 74330

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.414

Alfa AF: 0.394 Hom.: 6502

Bravo AF: 0.363

Asia WGS AF: 0.578 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs788261; hg19: chr10-43437970;