Variant 12-102384996-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000626826.1(HELLPAR):n.187412C>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 0.557 in 151,722 control chromosomes in the GnomAD database, including 24,104 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 0.56 ( 24100 hom., cov: 30)

Exomes 𝑓: 0.69 ( 4 hom. )

Consequence

HELLPAR
ENST00000626826.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.600

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02456	XR_007063427.1 linkuse as main transcript	n.697-19117C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
HELLPAR	ENST00000626826.1 linkuse as main transcript	n.187412C>T	non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1 linkuse as main transcript	n.1066+36064C>T	intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1 linkuse as main transcript	n.449+36064C>T	intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.557

AC:

84396

AN:

151588

Hom.:

24058

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.483

Gnomad AMR

AF:

0.478

Gnomad ASJ

AF:

0.450

Gnomad EAS

AF:

0.676

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.595

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.507

Gnomad OTH

AF:

0.551

GnomAD4 exome

AF:

0.688

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.625

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.557

AC:

84505

AN:

151706

Hom.:

24100

Cov.:

AF XY:

0.558

AC XY:

41350

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.479

Gnomad4 ASJ

AF:

0.450

Gnomad4 EAS

AF:

0.676

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.595

Gnomad4 NFE

AF:

0.507

Gnomad4 OTH

AF:

0.555

Alfa

AF:

0.495

Hom.:

14758

Bravo

AF:

0.559

Asia WGS

AF:

0.592

AC:

2052

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.70

DANN

Benign

0.60

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over