10-128912659-C-T

Position:

• chr10-128912659-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.139 in 152,160 control chromosomes in the GnomAD database, including 1,527 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 (1527 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.139 AC: 21106 AN: 152042 Hom.: 1525 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.139 AC: 21117 AN: 152160 Hom.: 1527 Cov.: 33 AF XY: 0.138 AC XY: 10284 AN XY: 74408

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.165

Alfa AF: 0.140 Hom.: 3116

Bravo AF: 0.139

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085203; hg19: chr10-130710923;