chr12-113014676-G-A

Variant names:

• chr12-113014676-G-A
• rs1293739
• ENST00000552784.1:n.353+2723C>T

Variant summary

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

The ENST00000552784.1(ENSG00000257452):​n.353+2723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,086 control chromosomes in the GnomAD database, including 4,597 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 0.24 (4597 hom., cov: 32)
• Consequence: ENSG00000257452 ENST00000552784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 6 publications found

Genes affected

ENSG00000257452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 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
ENSG00000257452	ENST00000552784.1	n.353+2723C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36298 AN: 151968 Hom.: 4596 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.239 AC: 36310 AN: 152086 Hom.: 4597 Cov.: 32 AF XY: 0.244 AC XY: 18122 AN XY: 74362

African (AFR) AF: 0.184 AC: 7644 AN: 41486

American (AMR) AF: 0.242 AC: 3701 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2437 AN: 5166

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4816

European-Finnish (FIN) AF: 0.317 AC: 3361 AN: 10588

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16470 AN: 67962

Other (OTH) AF: 0.231 AC: 487 AN: 2112

Alfa AF: 0.244 Hom.: 2475

Bravo AF: 0.233

Asia WGS AF: 0.363 AC: 1259 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1293739; hg19: chr12-113452481;