dbSNP rs10493332: LINC01739:n.253+17363C>T (chr1-63057067-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000748522.1(LINC01739):n.253+17363C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,158 control chromosomes in the GnomAD database, including 1,568 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 0.13 ( 1568 hom., cov: 32)

Consequence

LINC01739
ENST00000748522.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0770

Publications

3 publications found

Variant links:

Genes affected

LINC01739 (HGNC:52527): (long intergenic non-protein coding RNA 1739)

LINC01739 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01739	ENST00000748522.1 link	n.253+17363C>T	intron_variant	Intron 1 of 1
LINC01739	ENST00000748523.1 link	n.192+17363C>T	intron_variant	Intron 1 of 4
LINC01739	ENST00000748524.1 link	n.104+17363C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20339

AN:

152040

Hom.:

1562

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.0879

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.158

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

GnomAD4 genome

AF:

0.134

AC:

20359

AN:

152158

Hom.:

1568

Cov.:

AF XY:

0.129

AC XY:

9585

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.103

AC:

4271

AN:

41520

American (AMR)

AF:

0.128

AC:

1955

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

724

AN:

3468

East Asian (EAS)

AF:

0.00232

AC:

AN:

5182

South Asian (SAS)

AF:

0.128

AC:

618

AN:

4818

European-Finnish (FIN)

AF:

0.0879

AC:

930

AN:

10578

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11400

AN:

67990

Other (OTH)

AF:

0.161

AC:

339

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

893

1786

2679

3572

4465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.143

Hom.:

941

Bravo

AF:

0.137

Asia WGS

AF:

0.0830

AC:

286

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.0

(source)

DANN

Benign

0.69

PhyloP100

-0.077

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