10-45373001-G-T

Variant names:

• chr10-45373001-G-T
• rs6593482

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 0.168 in 152,094 control chromosomes in the GnomAD database, including 2,217 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 0.17 (2217 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 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: 0.168 AC: 25503 AN: 151974 Hom.: 2210 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.168 AC: 25541 AN: 152094 Hom.: 2217 Cov.: 33 AF XY: 0.169 AC XY: 12592 AN XY: 74334

African (AFR) AF: 0.177 AC: 7326 AN: 41462

American (AMR) AF: 0.134 AC: 2048 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3466

East Asian (EAS) AF: 0.182 AC: 946 AN: 5186

South Asian (SAS) AF: 0.189 AC: 912 AN: 4826

European-Finnish (FIN) AF: 0.195 AC: 2058 AN: 10564

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11072 AN: 67990

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.159 Hom.: 6266

Bravo AF: 0.163

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6593482; hg19: chr10-45868449;