Genetic Variant ENSG00000258535:n.1283C>T (chr14-51766558-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.898

Publications

16 publications found

Variant links:

Genes affected

ENSG00000258535 (HGNC:):

ENSG00000258535 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927598	XR_002957605.2 link	n.743C>T		non_coding_transcript_exon_variant	Exon 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258535	ENST00000553312.1 link	n.1283C>T		non_coding_transcript_exon_variant	Exon 1 of 10	1
ENSG00000293790	ENST00000719071.1 link	n.106-2576G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

41834

AN:

151846

Hom.:

6810

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.313

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.375

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.613

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.275

AC:

41830

AN:

151964

Hom.:

6808

Cov.:

AF XY:

0.276

AC XY:

20463

AN XY:

74242

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1450

2899

4349

5798

7248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.9

(source)

DANN

Benign

0.38

PhyloP100

0.90

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over