Genetic Variant LINC00964:n.1475C>T (chr8-124944074-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 ENST00000510897.7(LINC00964):n.1475C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 152,240 control chromosomes in the GnomAD database, including 832 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 0.069 ( 832 hom., cov: 32)

Exomes 𝑓: 0.019 ( 0 hom. )

Consequence

LINC00964
ENST00000510897.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.856

Publications

2 publications found

Variant links:

Genes affected

LINC00964 (HGNC:27226): (long intergenic non-protein coding RNA 964)

LINC00964 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00964	NR_027321.1 link	n.1522C>T		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00964	ENST00000510897.7 link	n.1475C>T	non_coding_transcript_exon_variant	Exon 2 of 4	1
LINC00964	ENST00000655947.1 link	n.163C>T	non_coding_transcript_exon_variant	Exon 1 of 4
LINC00964	ENST00000661433.1 link	n.720C>T	non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0685

AC:

10409

AN:

152016

Hom.:

815

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.0496

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.0846

Gnomad FIN

AF:

0.00990

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.00782

Gnomad OTH

AF:

0.0828

GnomAD4 exome

AF:

0.0192

AC:

AN:

104

Hom.:

Cov.:

AF XY:

0.0286

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0128

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0687

AC:

10452

AN:

152136

Hom.:

832

Cov.:

AF XY:

0.0724

AC XY:

5384

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.114

AC:

4736

AN:

41494

American (AMR)

AF:

0.206

AC:

3144

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0496

AC:

172

AN:

3470

East Asian (EAS)

AF:

0.223

AC:

1148

AN:

5154

South Asian (SAS)

AF:

0.0836

AC:

401

AN:

4796

European-Finnish (FIN)

AF:

0.00990

AC:

105

AN:

10610

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00779

AC:

530

AN:

68004

Other (OTH)

AF:

0.0923

AC:

195

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

443

887

1330

1774

2217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0673

Hom.:

446

Bravo

AF:

0.0899

Asia WGS

AF:

0.207

AC:

717

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.35

(source)

DANN

Benign

0.41

PhyloP100

-0.86

Mutation Taster

=100/0

polymorphism (auto)

(source)

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