Genetic Variant LINC01997:n.456-9931C>T (chr3-169027386-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 ENST00000650951.1(LINC01997):n.456-9931C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 152,140 control chromosomes in the GnomAD database, including 712 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 0.058 ( 712 hom., cov: 30)

Consequence

LINC01997
ENST00000650951.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Publications

1 publications found

Variant links:

Genes affected

LINC01997 (HGNC:52831): (long intergenic non-protein coding RNA 1997)

LINC01997 links:

ENSG00000303122 (HGNC:):

ENSG00000303122 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01997	ENST00000650951.1 link	n.456-9931C>T		intron_variant	Intron 3 of 4
ENSG00000303122	ENST00000791975.1 link	n.196+4273G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0576

AC:

8758

AN:

152022

Hom.:

706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0400

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.199

Gnomad ASJ

AF:

0.0190

Gnomad EAS

AF:

0.309

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0131

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0235

Gnomad OTH

AF:

0.0621

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

GnomAD4 genome

AF:

0.0577

AC:

8777

AN:

152140

Hom.:

712

Cov.:

AF XY:

0.0612

AC XY:

4553

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0402

AC:

1670

AN:

41518

American (AMR)

AF:

0.199

AC:

3044

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0190

AC:

AN:

3466

East Asian (EAS)

AF:

0.309

AC:

1593

AN:

5148

South Asian (SAS)

AF:

0.109

AC:

527

AN:

4820

European-Finnish (FIN)

AF:

0.0131

AC:

139

AN:

10600

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0235

AC:

1596

AN:

68002

Other (OTH)

AF:

0.0615

AC:

130

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

370

740

1110

1480

1850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0479

Hom.:

828

Bravo

AF:

0.0732

Asia WGS

AF:

0.186

AC:

646

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.99

(source)

DANN

Benign

0.40

PhyloP100

-1.1

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