rs10764058

Variant names:

• chr10-35801595-A-C
• rs10764058

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 0.204 in 152,002 control chromosomes in the GnomAD database, including 5,719 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 0.20 (5719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.619
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30976 AN: 151884 Hom.: 5689 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.204 AC: 31058 AN: 152002 Hom.: 5719 Cov.: 32 AF XY: 0.199 AC XY: 14791 AN XY: 74310

African (AFR) AF: 0.493 AC: 20411 AN: 41370

American (AMR) AF: 0.118 AC: 1805 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.0567 AC: 293 AN: 5172

South Asian (SAS) AF: 0.119 AC: 571 AN: 4814

European-Finnish (FIN) AF: 0.0714 AC: 758 AN: 10612

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0942 AC: 6405 AN: 67958

Other (OTH) AF: 0.180 AC: 380 AN: 2110

Alfa AF: 0.136 Hom.: 636

Bravo AF: 0.220

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.80
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs10764058; hg19: chr10-36090523;