12-102384996-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

Genes affected

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

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

ACMG classification

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	UniProt
LINC02456	XR_007063427.1	n.697-19117C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HELLPAR	ENST00000626826.1	n.187412C>T		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.1066+36064C>T		intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1	n.449+36064C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84396 AN: 151588 Hom.: 24058 Cov.: 30

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: 11 AN: 16 Hom.: 4 Cov.: 0 AF XY: 0.750 AC XY: 9 AN XY: 12

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.: 30 AF XY: 0.558 AC XY: 41350 AN XY: 74170

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

Other links and lift over

dbSNP: rs2139573; hg19: chr12-102778774;