dbSNP rs13231337: LINC02889:n.159-36672T>C (chr7-17520206-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000451792.1(LINC02889):n.159-36672T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,172 control chromosomes in the GnomAD database, including 1,035 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 0.10 ( 1035 hom., cov: 32)

Consequence

LINC02889
ENST00000451792.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.540

Publications

0 publications found

Variant links:

Genes affected

LINC02889 (HGNC:55071): (long intergenic non-protein coding RNA 2889)

LINC02889 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 (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02889	NR_110013.1 link	n.159-36672T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02889	ENST00000451792.1 link	n.159-36672T>C	intron_variant	Intron 1 of 3	3
LINC02889	ENST00000454003.2 link	n.52+3891T>C	intron_variant	Intron 1 of 8	3
LINC02889	ENST00000636929.1 link	n.79+3891T>C	intron_variant	Intron 1 of 10	5

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15334

AN:

152054

Hom.:

1037

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0229

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.108

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

GnomAD4 genome

AF:

0.101

AC:

15331

AN:

152172

Hom.:

1035

Cov.:

AF XY:

0.106

AC XY:

7869

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0229

AC:

950

AN:

41540

American (AMR)

AF:

0.171

AC:

2608

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

451

AN:

3470

East Asian (EAS)

AF:

0.119

AC:

618

AN:

5180

South Asian (SAS)

AF:

0.212

AC:

1023

AN:

4820

European-Finnish (FIN)

AF:

0.142

AC:

1499

AN:

10584

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7821

AN:

67976

Other (OTH)

AF:

0.109

AC:

229

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

684

1368

2052

2736

3420

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.110

Hom.:

135

Bravo

AF:

0.0979

Asia WGS

AF:

0.150

AC:

520

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

4.8

(source)

DANN

Benign

0.53

PhyloP100

0.54

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