rs12570088

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.58178575A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0230

Gnomad4 AMR AF: 0.0250

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0472 Hom.: 136

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12570088; hg19: chr10-59938336;