rs17032384

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000626826.1(HELLPAR):​n.85552T>G 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 0.0374 in 152,238 control chromosomes in the GnomAD database, including 308 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 0.037 ( 308 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

HELLPAR
ENST00000626826.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.459
Variant links:
Genes affected
HELLPAR (HGNC:43984): (HELLP associated long non-coding RNA)
LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02456XR_007063427.1 linkuse as main transcriptn.341+838T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HELLPARENST00000626826.1 linkuse as main transcriptn.85552T>G non_coding_transcript_exon_variant 1/1
LINC02456ENST00000704346.1 linkuse as main transcriptn.711+838T>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0372
AC:
5657
AN:
152120
Hom.:
300
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.117
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0197
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0174
Gnomad FIN
AF:
0.00236
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.00435
Gnomad OTH
AF:
0.0301
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.0374
AC:
5696
AN:
152238
Hom.:
308
Cov.:
32
AF XY:
0.0367
AC XY:
2736
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.118
Gnomad4 AMR
AF:
0.0196
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0178
Gnomad4 FIN
AF:
0.00236
Gnomad4 NFE
AF:
0.00435
Gnomad4 OTH
AF:
0.0298
Alfa
AF:
0.00874
Hom.:
62
Bravo
AF:
0.0419
Asia WGS
AF:
0.0120
AC:
42
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.25
CADD
Benign
14
DANN
Benign
0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17032384; hg19: chr12-102676914; API