Genetic Variant LINC01241:n.889+5344A>G (chr9-25804287-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 ENST00000423326.2(LINC01241):n.889+5344A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,950 control chromosomes in the GnomAD database, including 35,682 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 0.67 ( 35681 hom., cov: 31)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

LINC01241
ENST00000423326.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.502

Publications

4 publications found

Variant links:

Genes affected

LINC01241 (HGNC:49804): (long intergenic non-protein coding RNA 1241)

LINC01241 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01241	NR_121604.1 link	n.889+5344A>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01241	ENST00000423326.2 link	n.889+5344A>G	intron_variant	Intron 5 of 5	1
LINC01241	ENST00000627303.1 link	n.73+28A>G	intron_variant	Intron 1 of 2	4
LINC01241	ENST00000654259.1 link	n.959+1768A>G	intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.666

AC:

101081

AN:

151826

Hom.:

35621

Cov.:

show subpopulations

Gnomad AFR

AF:

0.915

Gnomad AMI

AF:

0.712

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.596

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.635

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.666

AC:

101200

AN:

151944

Hom.:

35681

Cov.:

AF XY:

0.667

AC XY:

49498

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.915

AC:

37955

AN:

41478

American (AMR)

AF:

0.633

AC:

9666

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.520

AC:

1803

AN:

3470

East Asian (EAS)

AF:

0.612

AC:

3154

AN:

5156

South Asian (SAS)

AF:

0.594

AC:

2861

AN:

4816

European-Finnish (FIN)

AF:

0.596

AC:

6278

AN:

10530

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.550

AC:

37334

AN:

67920

Other (OTH)

AF:

0.639

AC:

1346

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1539

3077

4616

6154

7693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.591

Hom.:

39981

Bravo

AF:

0.681

Asia WGS

AF:

0.649

AC:

2258

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.2

(source)

DANN

Benign

0.48

PhyloP100

-0.50

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