10-91758576-C-T

Variant names:

• chr10-91758576-C-T
• rs10509635

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 0.104 in 147,520 control chromosomes in the GnomAD database, including 857 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 0.10 (857 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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: 0.104 AC: 15337 AN: 147400 Hom.: 854 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0177

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0686

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.104 AC: 15358 AN: 147520 Hom.: 857 Cov.: 31 AF XY: 0.107 AC XY: 7674 AN XY: 71630

African (AFR) AF: 0.107 AC: 4289 AN: 40120

American (AMR) AF: 0.145 AC: 2105 AN: 14552

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 309 AN: 3458

East Asian (EAS) AF: 0.206 AC: 1002 AN: 4866

South Asian (SAS) AF: 0.157 AC: 706 AN: 4508

European-Finnish (FIN) AF: 0.0993 AC: 950 AN: 9568

Middle Eastern (MID) AF: 0.0603 AC: 17 AN: 282

European-Non Finnish (NFE) AF: 0.0855 AC: 5749 AN: 67202

Other (OTH) AF: 0.104 AC: 215 AN: 2062

Alfa AF: 0.0882 Hom.: 84

Bravo AF: 0.107

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10509635; hg19: chr10-93518333;