rs12783252

chr10-119472942-G-A

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 0.0754 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0409

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0953 Hom.: 1048

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12783252; hg19: chr10-121232454;