rs112125027

Variant names:

• chr10-52370993-A-G
• rs112125027

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 0.0492 in 152,158 control chromosomes in the GnomAD database, including 291 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 0.049 (291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 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: 0.0491 AC: 7468 AN: 152042 Hom.: 290 Cov.: 32

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0492 AC: 7484 AN: 152158 Hom.: 291 Cov.: 32 AF XY: 0.0515 AC XY: 3829 AN XY: 74380

African (AFR) AF: 0.0191 AC: 793 AN: 41508

American (AMR) AF: 0.0311 AC: 476 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3468

East Asian (EAS) AF: 0.135 AC: 701 AN: 5174

South Asian (SAS) AF: 0.162 AC: 779 AN: 4814

European-Finnish (FIN) AF: 0.0488 AC: 516 AN: 10578

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3846 AN: 68012

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.0483 Hom.: 30

Bravo AF: 0.0449

Asia WGS AF: 0.150 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.71
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs112125027; hg19: chr10-54130753;