chr10-100368255-T-C

Variant names:

• chr10-100368255-T-C
• rs490726

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 0.243 in 152,176 control chromosomes in the GnomAD database, including 5,413 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 0.24 (5413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36925 AN: 152058 Hom.: 5377 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.243 AC: 37003 AN: 152176 Hom.: 5413 Cov.: 33 AF XY: 0.243 AC XY: 18108 AN XY: 74402

African (AFR) AF: 0.398 AC: 16522 AN: 41498

American (AMR) AF: 0.159 AC: 2435 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1190 AN: 5184

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1921 AN: 10580

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12024 AN: 68012

Other (OTH) AF: 0.212 AC: 447 AN: 2106

Alfa AF: 0.211 Hom.: 822

Bravo AF: 0.244

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs490726; hg19: chr10-102128012;