chr12-115621878-C-T

Variant names:

• chr12-115621878-C-T
• rs12813282
• ENST00000551940.1:n.91-1716G>A

Variant summary

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

The ENST00000551940.1(ENSG00000257407):​n.91-1716G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,998 control chromosomes in the GnomAD database, including 25,253 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 0.57 (25253 hom., cov: 32)
• Consequence: ENSG00000257407 ENST00000551940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 1 publications found

Genes affected

ENSG00000257407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370002	NR_188486.1	n.236+18015G>A		intron_variant	Intron 2 of 5
LOC105370002	NR_188487.1	n.236+18015G>A		intron_variant	Intron 2 of 5
LOC105370003	XR_945388.3	n.119-113464G>A		intron_variant	Intron 1 of 3
LOC105370003	XR_945389.3	n.119-113464G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257407	ENST00000551940.1	n.91-1716G>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86755 AN: 151880 Hom.: 25229 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.571 AC: 86825 AN: 151998 Hom.: 25253 Cov.: 32 AF XY: 0.570 AC XY: 42360 AN XY: 74276

African (AFR) AF: 0.506 AC: 20950 AN: 41438

American (AMR) AF: 0.453 AC: 6918 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2449 AN: 5144

South Asian (SAS) AF: 0.617 AC: 2966 AN: 4810

European-Finnish (FIN) AF: 0.662 AC: 6994 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42600 AN: 67980

Other (OTH) AF: 0.564 AC: 1191 AN: 2112

Alfa AF: 0.578 Hom.: 4675

Bravo AF: 0.549

Asia WGS AF: 0.541 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.86
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12813282; hg19: chr12-116059683;