10-42844682-T-C

Variant names:

• chr10-42844682-T-C
• rs2744088

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 0.866 in 151,956 control chromosomes in the GnomAD database, including 57,087 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 (57087 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131423 AN: 151838 Hom.: 57035 Cov.: 30

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.858

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: 131534 AN: 151956 Hom.: 57087 Cov.: 30 AF XY: 0.866 AC XY: 64311 AN XY: 74272

African (AFR) AF: 0.927 AC: 38439 AN: 41464

American (AMR) AF: 0.847 AC: 12935 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3020 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4421 AN: 5156

South Asian (SAS) AF: 0.827 AC: 3962 AN: 4792

European-Finnish (FIN) AF: 0.863 AC: 9098 AN: 10546

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56701 AN: 67942

Other (OTH) AF: 0.866 AC: 1830 AN: 2114

Alfa AF: 0.854 Hom.: 9668

Bravo AF: 0.867

Asia WGS AF: 0.820 AC: 2853 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.64
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2744088; hg19: chr10-43340130;