14-51766558-C-T

Position:

• chr14-51766558-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553312.1(ENSG00000258535):​n.1283C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,984 control chromosomes in the GnomAD database, including 6,809 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 0.28 (6808 hom., cov: 31)
  • Exomes 𝑓: 0.30 (1 hom.)
• Consequence: ENSG00000258535 ENST00000553312.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

Genes affected

ENSG00000258535 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927598	XR_002957605.2	n.743C>T		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258535	ENST00000553312.1	n.1283C>T		non_coding_transcript_exon_variant	1/10	1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41834 AN: 151846 Hom.: 6810 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.342

GnomAD4 exome AF: 0.300 AC: 6 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.313 AC XY: 5 AN XY: 16

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.275 AC: 41830 AN: 151964 Hom.: 6808 Cov.: 31 AF XY: 0.276 AC XY: 20463 AN XY: 74242

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.340

Alfa AF: 0.329 Hom.: 9130

Bravo AF: 0.286

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11626056; hg19: chr14-52233276;