10-58960480-G-T

Position:

• chr10-58960480-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0815

Gnomad4 SAS AF: 0.0356

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.133

Alfa AF: 0.151 Hom.: 239

Bravo AF: 0.135

Asia WGS AF: 0.0780 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11006325; hg19: chr10-60720240;