10-42965426-C-T

Variant names:

• chr10-42965426-C-T
• rs2185792

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 0.424 in 152,122 control chromosomes in the GnomAD database, including 14,003 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 0.42 (14003 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64519 AN: 152004 Hom.: 14000 Cov.: 34

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.424 AC: 64550 AN: 152122 Hom.: 14003 Cov.: 34 AF XY: 0.424 AC XY: 31495 AN XY: 74352

African (AFR) AF: 0.510 AC: 21140 AN: 41474

American (AMR) AF: 0.439 AC: 6712 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5172

South Asian (SAS) AF: 0.424 AC: 2045 AN: 4822

European-Finnish (FIN) AF: 0.370 AC: 3915 AN: 10586

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26386 AN: 67996

Other (OTH) AF: 0.419 AC: 885 AN: 2114

Alfa AF: 0.421 Hom.: 1839

Bravo AF: 0.431

Asia WGS AF: 0.352 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2185792; hg19: chr10-43460874;