10-58952916-G-C

Variant names:

• chr10-58952916-G-C
• rs7089764

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 0.169 in 151,414 control chromosomes in the GnomAD database, including 2,414 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 0.17 (2414 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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: 0.169 AC: 25524 AN: 151296 Hom.: 2412 Cov.: 30

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.169 AC: 25549 AN: 151414 Hom.: 2414 Cov.: 30 AF XY: 0.167 AC XY: 12368 AN XY: 73916

African (AFR) AF: 0.236 AC: 9732 AN: 41180

American (AMR) AF: 0.128 AC: 1952 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3468

East Asian (EAS) AF: 0.0814 AC: 417 AN: 5124

South Asian (SAS) AF: 0.0379 AC: 181 AN: 4770

European-Finnish (FIN) AF: 0.177 AC: 1858 AN: 10474

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10061 AN: 67864

Other (OTH) AF: 0.155 AC: 326 AN: 2104

Alfa AF: 0.0745 Hom.: 99

Bravo AF: 0.171

Asia WGS AF: 0.0870 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs7089764; hg19: chr10-60712676;