10-90865388-C-T

Position:

• chr10-90865388-C-T

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 0.159 in 151,934 control chromosomes in the GnomAD database, including 2,899 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 0.16 (2899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24060 AN: 151816 Hom.: 2891 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.159 AC: 24092 AN: 151934 Hom.: 2899 Cov.: 32 AF XY: 0.162 AC XY: 12038 AN XY: 74280

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0902

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.151

Alfa AF: 0.117 Hom.: 389

Bravo AF: 0.171

Asia WGS AF: 0.222 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7100129; hg19: chr10-92625145;