chr10-94938063-G-T

Variant names:

• chr10-94938063-G-T
• rs9332100

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 0.0899 in 152,006 control chromosomes in the GnomAD database, including 780 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 0.090 (780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0900 AC: 13666 AN: 151888 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0899 AC: 13661 AN: 152006 Hom.: 780 Cov.: 32 AF XY: 0.0894 AC XY: 6638 AN XY: 74276

African (AFR) AF: 0.0235 AC: 977 AN: 41498

American (AMR) AF: 0.0982 AC: 1498 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3468

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5162

South Asian (SAS) AF: 0.0395 AC: 190 AN: 4810

European-Finnish (FIN) AF: 0.134 AC: 1408 AN: 10538

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8700 AN: 67956

Other (OTH) AF: 0.110 AC: 232 AN: 2106

Alfa AF: 0.0932 Hom.: 251

Bravo AF: 0.0865

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.23
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs9332100; hg19: chr10-96697820;