10-42942522-T-C

Variant names:

• chr10-42942522-T-C
• rs788261

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;