12-54682812-C-G

Variant names:

• chr12-54682812-C-G
• rs931585
• ENST00000552524.1:n.-161C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000552524.1(ENSG00000257634):​n.-161C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. 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: ENSG00000257634 ENST00000552524.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849
• Publications: 1 publications found

Genes affected

ENSG00000257634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552524.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000257634	ENST00000552524.1	TSL:3	n.-161C>G		upstream_gene	N/A

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

African (AFR) AF: 0.271 AC: 11209 AN: 41432

American (AMR) AF: 0.425 AC: 6494 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2913 AN: 5164

South Asian (SAS) AF: 0.299 AC: 1436 AN: 4804

European-Finnish (FIN) AF: 0.340 AC: 3595 AN: 10586

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18234 AN: 67968

Other (OTH) AF: 0.304 AC: 641 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.79
PhyloP100		0.85

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs931585;

hg19: chr12-55076596;