10-99558882-C-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 0.589 in 152,070 control chromosomes in the GnomAD database, including 26,826 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 0.59 (26826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89484 AN: 151952 Hom.: 26796 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.589 AC: 89565 AN: 152070 Hom.: 26826 Cov.: 32 AF XY: 0.590 AC XY: 43877 AN XY: 74320

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.565

Alfa AF: 0.581 Hom.: 4460

Bravo AF: 0.599

Asia WGS AF: 0.630 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.4
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7913135; hg19: chr10-101318639;