10-42976127-C-T

Variant names:

• chr10-42976127-C-T
• rs10900290

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 0.179 in 152,000 control chromosomes in the GnomAD database, including 2,860 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 0.18 (2860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.179 AC: 27199 AN: 151882 Hom.: 2860 Cov.: 32

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.179 AC: 27201 AN: 152000 Hom.: 2860 Cov.: 32 AF XY: 0.182 AC XY: 13556 AN XY: 74296

African (AFR) AF: 0.0915 AC: 3798 AN: 41488

American (AMR) AF: 0.253 AC: 3869 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1671 AN: 5146

South Asian (SAS) AF: 0.331 AC: 1586 AN: 4796

European-Finnish (FIN) AF: 0.155 AC: 1637 AN: 10566

Middle Eastern (MID) AF: 0.266 AC: 77 AN: 290

European-Non Finnish (NFE) AF: 0.193 AC: 13135 AN: 67944

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.194 Hom.: 5324

Bravo AF: 0.179

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.4
DANN	Benign	0.93
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10900290; hg19: chr10-43471575;