dbSNP rs10519517: LINC00992:n.535-468C>A (chr5-117576780-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000828611.1(LINC00992):n.535-468C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 152,202 control chromosomes in the GnomAD database, including 1,402 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 0.081 ( 1402 hom., cov: 32)

Consequence

LINC00992
ENST00000828611.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.749

Publications

0 publications found

Variant links:

Genes affected

LINC00992 (HGNC:48943): (long intergenic non-protein coding RNA 992)

LINC00992 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 = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00992	NR_046089.1 link	n.595-468C>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00992	ENST00000828611.1 link	n.535-468C>A		intron_variant	Intron 3 of 3
LINC00992	ENST00000828612.1 link	n.588-468C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0809

AC:

12307

AN:

152084

Hom.:

1403

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0361

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0205

Gnomad FIN

AF:

0.00736

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0703

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

GnomAD4 genome

AF:

0.0810

AC:

12328

AN:

152202

Hom.:

1402

Cov.:

AF XY:

0.0776

AC XY:

5776

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.257

AC:

10672

AN:

41482

American (AMR)

AF:

0.0360

AC:

551

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00259

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5190

South Asian (SAS)

AF:

0.0209

AC:

101

AN:

4828

European-Finnish (FIN)

AF:

0.00736

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0105

AC:

714

AN:

68012

Other (OTH)

AF:

0.0696

AC:

147

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

476

953

1429

1906

2382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0439

Hom.:

237

Bravo

AF:

0.0921

Asia WGS

AF:

0.0210

AC:

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

2.7

(source)

DANN

Benign

0.76

PhyloP100

-0.75

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