10-58960480-G-T

Variant names:

• chr10-58960480-G-T
• rs11006325

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 0.137 in 152,116 control chromosomes in the GnomAD database, including 1,565 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 0.14 (1565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 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: 0.137 AC: 20880 AN: 151998 Hom.: 1563 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.137 AC: 20897 AN: 152116 Hom.: 1565 Cov.: 32 AF XY: 0.136 AC XY: 10149 AN XY: 74358

African (AFR) AF: 0.129 AC: 5336 AN: 41504

American (AMR) AF: 0.114 AC: 1735 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 868 AN: 3464

East Asian (EAS) AF: 0.0815 AC: 421 AN: 5166

South Asian (SAS) AF: 0.0356 AC: 172 AN: 4828

European-Finnish (FIN) AF: 0.179 AC: 1891 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10047 AN: 67988

Other (OTH) AF: 0.133 AC: 280 AN: 2112

Alfa AF: 0.150 Hom.: 250

Bravo AF: 0.135

Asia WGS AF: 0.0780 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.51
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11006325; hg19: chr10-60720240;