10-90391205-C-T

Variant names:

• chr10-90391205-C-T
• rs12355470

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 0.505 in 151,890 control chromosomes in the GnomAD database, including 20,199 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 0.51 (20199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 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: 0.505 AC: 76656 AN: 151772 Hom.: 20181 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.505 AC: 76711 AN: 151890 Hom.: 20199 Cov.: 32 AF XY: 0.498 AC XY: 36993 AN XY: 74220

African (AFR) AF: 0.373 AC: 15437 AN: 41416

American (AMR) AF: 0.516 AC: 7873 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1699 AN: 5160

South Asian (SAS) AF: 0.374 AC: 1800 AN: 4810

European-Finnish (FIN) AF: 0.498 AC: 5234 AN: 10516

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41079 AN: 67930

Other (OTH) AF: 0.500 AC: 1058 AN: 2114

Alfa AF: 0.576 Hom.: 42522

Bravo AF: 0.503

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.53
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs12355470; hg19: chr10-92150962;