rs10748582

Variant names:

• chr10-92717462-T-A
• rs10748582

Your query was ambiguous. Multiple possible variants found:

• chr10-92717462-T-A
• chr10-92717462-T-G

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 0.32 in 152,204 control chromosomes in the GnomAD database, including 9,908 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 0.32 (9908 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.320 AC: 48617 AN: 152086 Hom.: 9909 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.320 AC: 48633 AN: 152204 Hom.: 9908 Cov.: 32 AF XY: 0.326 AC XY: 24238 AN XY: 74414

African (AFR) AF: 0.0919 AC: 3819 AN: 41560

American (AMR) AF: 0.376 AC: 5745 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.806 AC: 4176 AN: 5184

South Asian (SAS) AF: 0.546 AC: 2639 AN: 4834

European-Finnish (FIN) AF: 0.391 AC: 4136 AN: 10566

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25623 AN: 67978

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.216 Hom.: 521

Bravo AF: 0.313

Asia WGS AF: 0.584 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs10748582; hg19: chr10-94477219;