10-99558882-C-T

Variant names:

• chr10-99558882-C-T
• rs7913135

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 0.589 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.681 AC: 28274 AN: 41492

American (AMR) AF: 0.619 AC: 9463 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1720 AN: 3472

East Asian (EAS) AF: 0.630 AC: 3254 AN: 5162

South Asian (SAS) AF: 0.637 AC: 3074 AN: 4826

European-Finnish (FIN) AF: 0.531 AC: 5609 AN: 10556

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36288 AN: 67968

Other (OTH) AF: 0.565 AC: 1192 AN: 2108

Alfa AF: 0.585 Hom.: 5300

Bravo AF: 0.599

Asia WGS AF: 0.630 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.73
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs7913135; hg19: chr10-101318639;