rs12812339

Variant names:

• chr12-4381679-A-C
• rs12812339
• ENST00000674624.1:n.*1204+15397A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000674624.1(ENSG00000285901):​n.*1204+15397A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,192 control chromosomes in the GnomAD database, including 4,221 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 0.21 (4221 hom., cov: 32)
• Consequence: ENSG00000285901 ENST00000674624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 8 publications found

Genes affected

ENSG00000285901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674624.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285901	ENST00000674624.1		n.*1204+15397A>C		intron	N/A	ENSP00000501898.1
	ENSG00000285901	ENST00000648100.1		n.*1967+15397A>C		intron	N/A	ENSP00000497536.1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31260 AN: 152074 Hom.: 4221 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.0327

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.205 AC: 31252 AN: 152192 Hom.: 4221 Cov.: 32 AF XY: 0.204 AC XY: 15206 AN XY: 74394

African (AFR) AF: 0.0531 AC: 2209 AN: 41564

American (AMR) AF: 0.180 AC: 2750 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.0326 AC: 169 AN: 5186

South Asian (SAS) AF: 0.195 AC: 940 AN: 4832

European-Finnish (FIN) AF: 0.311 AC: 3282 AN: 10558

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20069 AN: 67978

Other (OTH) AF: 0.209 AC: 440 AN: 2110

Alfa AF: 0.227 Hom.: 1726

Bravo AF: 0.188

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.62
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs12812339; hg19: chr12-4490845;