14-55758517-C-T

Variant names:

• chr14-55758517-C-T
• rs8014482
• ENST00000554458.1:n.75+10235C>T

Variant summary

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

The ENST00000554458.1(ENSG00000258784):​n.75+10235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,010 control chromosomes in the GnomAD database, including 3,615 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 0.20 (3615 hom., cov: 32)
• Consequence: ENSG00000258784 ENST00000554458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 6 publications found

Genes affected

ENSG00000258784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 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
ENSG00000258784	ENST00000554458.1	n.75+10235C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30757 AN: 151892 Hom.: 3608 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.203 AC: 30782 AN: 152010 Hom.: 3615 Cov.: 32 AF XY: 0.205 AC XY: 15255 AN XY: 74302

African (AFR) AF: 0.255 AC: 10566 AN: 41432

American (AMR) AF: 0.228 AC: 3482 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2511 AN: 5172

South Asian (SAS) AF: 0.225 AC: 1081 AN: 4806

European-Finnish (FIN) AF: 0.170 AC: 1800 AN: 10564

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10108 AN: 67988

Other (OTH) AF: 0.204 AC: 429 AN: 2104

Alfa AF: 0.173 Hom.: 8839

Bravo AF: 0.212

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs8014482; hg19: chr14-56225235;