14-51766558-C-T

Variant names:

• chr14-51766558-C-T
• rs11626056
• ENST00000553312.1:n.1283C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

Genes affected

ENSG00000258535 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553312.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258535	ENST00000553312.1	TSL:1	n.1283C>T		non_coding_transcript_exon	Exon 1 of 10
	ENSG00000293790	ENST00000719071.1		n.106-2576G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.375 AC: 6 AN: 16

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.108 AC: 4476 AN: 41458

American (AMR) AF: 0.421 AC: 6419 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2212 AN: 5156

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2505 AN: 10558

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22385 AN: 67936

Other (OTH) AF: 0.340 AC: 715 AN: 2106

Alfa AF: 0.314 Hom.: 14885

Bravo AF: 0.286

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.38
PhyloP100		0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11626056;

hg19: chr14-52233276;