rs12783252

Variant names:

• chr10-119472942-G-A
• rs12783252

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 0.0754 in 152,138 control chromosomes in the GnomAD database, including 609 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 0.075 (609 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0996 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: 0.0755 AC: 11482 AN: 152020 Hom.: 609 Cov.: 32

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0754 AC: 11474 AN: 152138 Hom.: 609 Cov.: 32 AF XY: 0.0775 AC XY: 5759 AN XY: 74348

African (AFR) AF: 0.0176 AC: 731 AN: 41524

American (AMR) AF: 0.0730 AC: 1116 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0409 AC: 197 AN: 4818

European-Finnish (FIN) AF: 0.170 AC: 1798 AN: 10552

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6908 AN: 67990

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0923 Hom.: 1289

Bravo AF: 0.0652

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.37
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs12783252; hg19: chr10-121232454;