rs10744085

Variant names:

• chr12-15042070-G-A
• rs10744085

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 0.149 in 152,158 control chromosomes in the GnomAD database, including 1,735 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 0.15 (1735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 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: 0.149 AC: 22612 AN: 152040 Hom.: 1731 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0757

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.149 AC: 22630 AN: 152158 Hom.: 1735 Cov.: 32 AF XY: 0.149 AC XY: 11101 AN XY: 74408

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0758

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.147

Alfa AF: 0.153 Hom.: 2784

Bravo AF: 0.143

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10744085; hg19: chr12-15195004;