Genetic Variant ENST00000565955.1:n.886C>T (chr1-109896858-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 ENST00000565955.1(ENSG00000261055):n.886C>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 0.773 in 152,184 control chromosomes in the GnomAD database, including 45,849 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 0.77 ( 45844 hom., cov: 33)

Exomes 𝑓: 0.78 ( 5 hom. )

Consequence

ENSG00000261055
ENST00000565955.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Publications

9 publications found

Variant links:

Genes affected

ENSG00000261055 (HGNC:):

ENSG00000261055 links:

LINC01768 (HGNC:52558): (long intergenic non-protein coding RNA 1768)

LINC01768 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01768	XR_001738180.3 link	n.831-8849C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000261055	ENST00000565955.1 link	n.886C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000235005	ENST00000415166.2 link	n.115+696G>A	intron_variant	Intron 1 of 3	3
ENSG00000235005	ENST00000746442.1 link	n.147+696G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.773

AC:

117599

AN:

152048

Hom.:

45804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.692

Gnomad AMI

AF:

0.769

Gnomad AMR

AF:

0.824

Gnomad ASJ

AF:

0.774

Gnomad EAS

AF:

0.979

Gnomad SAS

AF:

0.879

Gnomad FIN

AF:

0.745

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.792

Gnomad OTH

AF:

0.804

GnomAD4 exome

AF:

0.778

AC:

AN:

Hom.:

Cov.:

AF XY:

0.786

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:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.900

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.563

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.773

AC:

117696

AN:

152166

Hom.:

45844

Cov.:

AF XY:

0.776

AC XY:

57685

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.692

AC:

28722

AN:

41482

American (AMR)

AF:

0.824

AC:

12619

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.774

AC:

2687

AN:

3472

East Asian (EAS)

AF:

0.979

AC:

5065

AN:

5176

South Asian (SAS)

AF:

0.877

AC:

4229

AN:

4820

European-Finnish (FIN)

AF:

0.745

AC:

7884

AN:

10586

Middle Eastern (MID)

AF:

0.769

AC:

226

AN:

294

European-Non Finnish (NFE)

AF:

0.792

AC:

53859

AN:

68000

Other (OTH)

AF:

0.806

AC:

1704

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1367

2735

4102

5470

6837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

870

1740

2610

3480

4350

<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:

0.789

Hom.:

119744

Bravo

AF:

0.775

Asia WGS

AF:

0.918

AC:

3190

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.22

(source)

DANN

Benign

0.59

PhyloP100

-1.5

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over