12-54682812-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.301 in 152,024 control chromosomes in the GnomAD database, including 7,317 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 0.30 (7317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 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: 0.301 AC: 45698 AN: 151906 Hom.: 7297 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.301 AC: 45757 AN: 152024 Hom.: 7317 Cov.: 32 AF XY: 0.308 AC XY: 22905 AN XY: 74332

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.304

Alfa AF: 0.182 Hom.: 382

Bravo AF: 0.310

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	18
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931585; hg19: chr12-55076596;