Genetic Variant LINC01965:n.136+87630T>C (chr2-103962075-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000537492.5(LINC01965):n.136+87630T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,126 control chromosomes in the GnomAD database, including 2,604 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 0.18 ( 2604 hom., cov: 32)

Consequence

LINC01965
ENST00000537492.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.495

Publications

5 publications found

Variant links:

Genes affected

LINC01965 (HGNC:52790): (long intergenic non-protein coding RNA 1965)

LINC01965 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01965	XR_001739621.2 link	n.157+87630T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01965	ENST00000537492.5 link	n.136+87630T>C	intron_variant	Intron 1 of 3	4
LINC01965	ENST00000544869.5 link	n.115+87630T>C	intron_variant	Intron 1 of 2	4
LINC01965	ENST00000688553.2 link	n.293+87630T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26893

AN:

152008

Hom.:

2601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.252

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.0980

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.177

AC:

26908

AN:

152126

Hom.:

2604

Cov.:

AF XY:

0.174

AC XY:

12911

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.252

AC:

10451

AN:

41478

American (AMR)

AF:

0.100

AC:

1528

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.218

AC:

757

AN:

3470

East Asian (EAS)

AF:

0.241

AC:

1238

AN:

5142

South Asian (SAS)

AF:

0.151

AC:

732

AN:

4832

European-Finnish (FIN)

AF:

0.0980

AC:

1040

AN:

10608

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10685

AN:

68006

Other (OTH)

AF:

0.154

AC:

325

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1113

2226

3339

4452

5565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<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:

0.170

Hom.:

1148

Bravo

AF:

0.180

Asia WGS

AF:

0.141

AC:

487

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.64

PhyloP100

0.49

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