Genetic Variant ENST00000412141.2: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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over