chr10-99558882-C-T

Variant names:

• chr10-99558882-C-T
• rs7913135

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;