rs12425376

Variant names:

• chr12-27975692-T-C
• rs12425376
• ENST00000825703.1:n.442T>C

Variant summary

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

The ENST00000825703.1(ENSG00000307399):​n.442T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,960 control chromosomes in the GnomAD database, including 14,464 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 0.43 (14464 hom., cov: 32)
• Consequence: ENSG00000307399 ENST00000825703.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 2 publications found

Genes affected

ENSG00000307399 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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
ENSG00000307399	ENST00000825703.1	n.442T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65313 AN: 151842 Hom.: 14430 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.430 AC: 65412 AN: 151960 Hom.: 14464 Cov.: 32 AF XY: 0.430 AC XY: 31953 AN XY: 74274

African (AFR) AF: 0.500 AC: 20727 AN: 41462

American (AMR) AF: 0.423 AC: 6466 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.561 AC: 2875 AN: 5128

South Asian (SAS) AF: 0.456 AC: 2189 AN: 4798

European-Finnish (FIN) AF: 0.353 AC: 3724 AN: 10556

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26616 AN: 67944

Other (OTH) AF: 0.418 AC: 884 AN: 2116

Alfa AF: 0.397 Hom.: 19123

Bravo AF: 0.440

Asia WGS AF: 0.467 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	15
DANN	Benign	0.39
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs12425376; hg19: chr12-28128625;