dbSNP rs1036736: 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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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