10-58153390-C-T

Variant names:

• chr10-58153390-C-T
• rs1819658

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 0.288 in 152,076 control chromosomes in the GnomAD database, including 7,291 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 0.29 (7291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 43 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 (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43791 AN: 151958 Hom.: 7278 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.288 AC: 43841 AN: 152076 Hom.: 7291 Cov.: 32 AF XY: 0.287 AC XY: 21346 AN XY: 74346

African (AFR) AF: 0.453 AC: 18794 AN: 41464

American (AMR) AF: 0.223 AC: 3405 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 685 AN: 3464

East Asian (EAS) AF: 0.455 AC: 2348 AN: 5166

South Asian (SAS) AF: 0.249 AC: 1198 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2215 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14463 AN: 67994

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.238 Hom.: 16106

Bravo AF: 0.299

Asia WGS AF: 0.292 AC: 1019 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	0.21
DANN	Benign	0.69
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1819658; hg19: chr10-59913151;