rs10744085

Variant names:

• chr12-15042070-G-A
• rs10744085

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 0.149 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.141 AC: 5857 AN: 41496

American (AMR) AF: 0.112 AC: 1709 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3466

East Asian (EAS) AF: 0.0758 AC: 393 AN: 5182

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1500 AN: 10584

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10599 AN: 67986

Other (OTH) AF: 0.147 AC: 311 AN: 2112

Alfa AF: 0.151 Hom.: 4439

Bravo AF: 0.143

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.15
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10744085; hg19: chr12-15195004;