12-115621878-C-T

Position:

• chr12-115621878-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000257407 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105370002	NR_188486.1	n.236+18015G>A		intron_variant
LOC105370002	NR_188487.1	n.236+18015G>A		intron_variant
LOC105370003	XR_945388.3	n.119-113464G>A		intron_variant
LOC105370003	XR_945389.3	n.119-113464G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257407	ENST00000551940.1	n.91-1716G>A		intron_variant		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

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.564

Alfa AF: 0.580 Hom.: 4566

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12813282; hg19: chr12-116059683;