Genetic Variant LINC00963:n.203+1909C>T (chr9-129495504-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 ENST00000412141.2(LINC00963):n.203+1909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,158 control chromosomes in the GnomAD database, including 10,726 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 0.35 ( 10721 hom., cov: 33)

Exomes 𝑓: 0.45 ( 5 hom. )

Consequence

LINC00963
ENST00000412141.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

7 publications found

Variant links:

Genes affected

LINC00963 (HGNC:48716): (long intergenic non-protein coding RNA 963)

LINC00963 links:

ENSG00000309757 (HGNC:):

ENSG00000309757 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
LINC00963	NR_038955.1 link	n.758+1909C>T	intron_variant	Intron 2 of 4
LOC124900275	XM_047424322.1 link	c.*222+1909C>T	intron_variant	Intron 2 of 2	XP_047280278.1
LOC124900275	XM_047424323.1 link	c.*225+1909C>T	intron_variant	Intron 2 of 2	XP_047280279.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00963	ENST00000412141.2 link	n.203+1909C>T	intron_variant	Intron 2 of 4	1
LINC00963	ENST00000419300.3 link	n.200+6205C>T	intron_variant	Intron 1 of 1	1
LINC00963	ENST00000444184.7 link	n.935+1909C>T	intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52512

AN:

151998

Hom.:

10728

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.426

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.455

Gnomad OTH

AF:

0.352

GnomAD4 exome

AF:

0.452

AC:

AN:

Hom.:

Cov.:

AF XY:

0.441

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.406

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.558

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.345

AC:

52509

AN:

152116

Hom.:

10721

Cov.:

AF XY:

0.346

AC XY:

25712

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.114

AC:

4724

AN:

41544

American (AMR)

AF:

0.400

AC:

6113

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.447

AC:

1551

AN:

3470

East Asian (EAS)

AF:

0.338

AC:

1743

AN:

5164

South Asian (SAS)

AF:

0.427

AC:

2056

AN:

4820

European-Finnish (FIN)

AF:

0.386

AC:

4080

AN:

10574

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.455

AC:

30911

AN:

67950

Other (OTH)

AF:

0.347

AC:

733

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1652

3303

4955

6606

8258

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

508

1016

1524

2032

2540

<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:

0.426

Hom.:

23897

Bravo

AF:

0.333

Asia WGS

AF:

0.339

AC:

1184

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.79

(source)

DANN

Benign

0.58

PhyloP100

-1.8

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