14-54106263-A-G

Variant names:

• chr14-54106263-A-G
• rs12432287
• ENST00000747857.1:n.595-14166T>C

Variant summary

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

The ENST00000747857.1(ENSG00000297427):​n.595-14166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,158 control chromosomes in the GnomAD database, including 26,025 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 0.56 (26025 hom., cov: 33)
• Consequence: ENSG00000297427 ENST00000747857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 3 publications found

Genes affected

ENSG00000297427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747857.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297427	ENST00000747857.1		n.595-14166T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84598 AN: 152040 Hom.: 26025 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.556 AC: 84611 AN: 152158 Hom.: 26025 Cov.: 33 AF XY: 0.561 AC XY: 41724 AN XY: 74360

African (AFR) AF: 0.273 AC: 11331 AN: 41518

American (AMR) AF: 0.561 AC: 8568 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2263 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2503 AN: 5174

South Asian (SAS) AF: 0.675 AC: 3255 AN: 4820

European-Finnish (FIN) AF: 0.752 AC: 7952 AN: 10580

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46752 AN: 67992

Other (OTH) AF: 0.578 AC: 1222 AN: 2114

Alfa AF: 0.659 Hom.: 14692

Bravo AF: 0.526

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.43
DANN	Benign	0.83
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs12432287; hg19: chr14-54572981;