dbSNP rs10860861: HELLPAR:n.194207C>T (chr12-102391791-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 ENST00000626826.1(HELLPAR):n.194207C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,078 control chromosomes in the GnomAD database, including 24,035 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 0.55 ( 24022 hom., cov: 31)

Exomes 𝑓: 0.55 ( 13 hom. )

Consequence

HELLPAR
ENST00000626826.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.323

Publications

9 publications found

Variant links:

Genes affected

HELLPAR (HGNC:43984): (HELLP associated long non-coding RNA)

HELLPAR links:

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

LINC02456 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1 link	n.697-12322C>T		intron_variant	Intron 6 of 12

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HELLPAR	ENST00000626826.1 link	n.194207C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02456	ENST00000635615.1 link	n.450-31280C>T	intron_variant	Intron 4 of 5	5
LINC02456	ENST00000704346.1 link	n.1067-31280C>T	intron_variant	Intron 9 of 10

Frequencies

GnomAD3 genomes

AF:

0.554

AC:

84143

AN:

151880

Hom.:

23973

Cov.:

show subpopulations

Gnomad AFR

AF:

0.693

Gnomad AMI

AF:

0.485

Gnomad AMR

AF:

0.479

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.629

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.560

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.497

Gnomad OTH

AF:

0.552

GnomAD4 exome

AF:

0.550

AC:

AN:

Hom.:

Cov.:

AF XY:

0.483

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.565

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.554

AC:

84259

AN:

151998

Hom.:

24022

Cov.:

AF XY:

0.553

AC XY:

41063

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.693

AC:

28729

AN:

41462

American (AMR)

AF:

0.480

AC:

7328

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

1542

AN:

3470

East Asian (EAS)

AF:

0.629

AC:

3239

AN:

5152

South Asian (SAS)

AF:

0.407

AC:

1964

AN:

4822

European-Finnish (FIN)

AF:

0.560

AC:

5912

AN:

10558

Middle Eastern (MID)

AF:

0.503

AC:

148

AN:

294

European-Non Finnish (NFE)

AF:

0.497

AC:

33787

AN:

67954

Other (OTH)

AF:

0.556

AC:

1170

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1830

3659

5489

7318

9148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

716

1432

2148

2864

3580

<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:

0.507

Hom.:

22855

Bravo

AF:

0.559

Asia WGS

AF:

0.567

AC:

1969

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.8

(source)

DANN

Benign

0.36

PhyloP100

0.32

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