12-69432249-A-G

Variant names:

• chr12-69432249-A-G
• rs10784780

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 0.548 in 151,778 control chromosomes in the GnomAD database, including 23,358 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 0.55 (23358 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.548 AC: 83124 AN: 151660 Hom.: 23332 Cov.: 30

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.548 AC: 83201 AN: 151778 Hom.: 23358 Cov.: 30 AF XY: 0.552 AC XY: 40945 AN XY: 74154

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.560

Alfa AF: 0.568 Hom.: 26533

Bravo AF: 0.542

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10784780; hg19: chr12-69826029;