rs10458664

Variant names:

• chr10-78802567-C-T
• rs10458664

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 0.146 in 152,268 control chromosomes in the GnomAD database, including 1,912 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 0.15 (1912 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 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: 0.146 AC: 22251 AN: 152150 Hom.: 1910 Cov.: 33

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.146 AC: 22266 AN: 152268 Hom.: 1912 Cov.: 33 AF XY: 0.148 AC XY: 11005 AN XY: 74444

African (AFR) AF: 0.0695 AC: 2887 AN: 41558

American (AMR) AF: 0.168 AC: 2575 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1447 AN: 5180

South Asian (SAS) AF: 0.296 AC: 1429 AN: 4826

European-Finnish (FIN) AF: 0.109 AC: 1159 AN: 10616

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11832 AN: 68016

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.155 Hom.: 250

Bravo AF: 0.144

Asia WGS AF: 0.239 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.70
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10458664; hg19: chr10-80562324;