dbSNP rs6841061: LINC02436:n.1499+6316G>A (chr4-185078389-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000509017.6(LINC02436):n.1499+6316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 518,070 control chromosomes in the GnomAD database, including 97,392 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 0.63 ( 30631 hom., cov: 33)

Exomes 𝑓: 0.60 ( 66761 hom. )

Consequence

LINC02436
ENST00000509017.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.423

Publications

5 publications found

Variant links:

Genes affected

LINC02436 (HGNC:53368): (long intergenic non-protein coding RNA 2436)

LINC02436 links:

ENSG00000307445 (HGNC:):

ENSG00000307445 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105377588	XR_002959837.1 link	n.890C>T	non_coding_transcript_exon_variant	Exon 2 of 3
LOC105377588	XR_939565.3 link	n.1236C>T	non_coding_transcript_exon_variant	Exon 4 of 5
LINC02436	NR_147059.2 link	n.1359+6316G>A	intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02436	ENST00000509017.6 link	n.1499+6316G>A	intron_variant	Intron 6 of 9	1
ENSG00000307445	ENST00000826339.1 link	n.954C>T	non_coding_transcript_exon_variant	Exon 2 of 3
LINC02436	ENST00000652785.1 link	n.394-7395G>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.630

AC:

95744

AN:

152012

Hom.:

30601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.690

Gnomad AMI

AF:

0.776

Gnomad AMR

AF:

0.581

Gnomad ASJ

AF:

0.753

Gnomad EAS

AF:

0.350

Gnomad SAS

AF:

0.568

Gnomad FIN

AF:

0.567

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.630

Gnomad OTH

AF:

0.648

GnomAD2 exomes

AF:

0.589

AC:

134859

AN:

228804

AF XY:

0.593

show subpopulations

Gnomad AFR exome

AF:

0.691

Gnomad AMR exome

AF:

0.524

Gnomad ASJ exome

AF:

0.745

Gnomad EAS exome

AF:

0.333

Gnomad FIN exome

AF:

0.566

Gnomad NFE exome

AF:

0.630

Gnomad OTH exome

AF:

0.613

GnomAD4 exome

AF:

0.598

AC:

218973

AN:

365940

Hom.:

66761

Cov.:

AF XY:

0.599

AC XY:

125683

AN XY:

209812

show subpopulations

African (AFR)

AF:

0.693

AC:

7258

AN:

10478

American (AMR)

AF:

0.521

AC:

18891

AN:

36228

Ashkenazi Jewish (ASJ)

AF:

0.745

AC:

8731

AN:

11712

East Asian (EAS)

AF:

0.331

AC:

4351

AN:

13164

South Asian (SAS)

AF:

0.576

AC:

38350

AN:

66568

European-Finnish (FIN)

AF:

0.565

AC:

9532

AN:

16864

Middle Eastern (MID)

AF:

0.705

AC:

2010

AN:

2850

European-Non Finnish (NFE)

AF:

0.624

AC:

119588

AN:

191502

Other (OTH)

AF:

0.619

AC:

10262

AN:

16574

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

4752

9504

14255

19007

23759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

822

1644

2466

3288

4110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.630

AC:

95822

AN:

152130

Hom.:

30631

Cov.:

AF XY:

0.623

AC XY:

46319

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.691

AC:

28672

AN:

41518

American (AMR)

AF:

0.580

AC:

8860

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.753

AC:

2613

AN:

3470

East Asian (EAS)

AF:

0.350

AC:

1812

AN:

5174

South Asian (SAS)

AF:

0.568

AC:

2741

AN:

4824

European-Finnish (FIN)

AF:

0.567

AC:

5981

AN:

10552

Middle Eastern (MID)

AF:

0.694

AC:

204

AN:

294

European-Non Finnish (NFE)

AF:

0.630

AC:

42865

AN:

67988

Other (OTH)

AF:

0.646

AC:

1366

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1816

3632

5448

7264

9080

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.629

Hom.:

25551

Bravo

AF:

0.634

Asia WGS

AF:

0.477

AC:

1661

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.45

(source)

DANN

Benign

0.60

PhyloP100

-0.42

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over