rs12570088

Variant names:

• chr10-58178575-A-G
• rs12570088

Your query was ambiguous. Multiple possible variants found:

• chr10-58178575-A-G
• chr10-58178575-A-T

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 0.043 in 152,204 control chromosomes in the GnomAD database, including 183 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 0.043 (183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0430 AC: 6535 AN: 152086 Hom.: 183 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0250

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0430 AC: 6539 AN: 152204 Hom.: 183 Cov.: 32 AF XY: 0.0453 AC XY: 3374 AN XY: 74412

African (AFR) AF: 0.0230 AC: 954 AN: 41540

American (AMR) AF: 0.0250 AC: 381 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3466

East Asian (EAS) AF: 0.137 AC: 711 AN: 5176

South Asian (SAS) AF: 0.102 AC: 494 AN: 4826

European-Finnish (FIN) AF: 0.0526 AC: 558 AN: 10614

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0452 AC: 3073 AN: 67998

Other (OTH) AF: 0.0374 AC: 79 AN: 2112

Alfa AF: 0.0464 Hom.: 408

Bravo AF: 0.0386

Asia WGS AF: 0.0740 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.65
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs12570088; hg19: chr10-59938336;