10-42942522-T-C

Variant names:

• chr10-42942522-T-C
• rs788261

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 0.365 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.193 AC: 8008 AN: 41486

American (AMR) AF: 0.481 AC: 7354 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3754 AN: 5146

South Asian (SAS) AF: 0.536 AC: 2580 AN: 4814

European-Finnish (FIN) AF: 0.405 AC: 4288 AN: 10584

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26490 AN: 67966

Other (OTH) AF: 0.414 AC: 872 AN: 2104

Alfa AF: 0.394 Hom.: 8582

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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs788261; hg19: chr10-43437970;