rs2946831

chr12-102393002-C-Achr12-102393002-C-Gchr12-102393002-C-T

Variant summary

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

The ENST00000626826.1(HELLPAR):n.195418C>A 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 0.914 in 152,262 control chromosomes in the GnomAD database, including 63,714 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 0.91 (63713 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.697-11111C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HELLPAR	ENST00000626826.1	n.195418C>A		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.1067-30069C>A		intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1	n.450-30069C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.914 AC: 139048 AN: 152142 Hom.: 63675 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.921

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.914 AC: 139142 AN: 152260 Hom.: 63713 Cov.: 32 AF XY: 0.915 AC XY: 68134 AN XY: 74444

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.922

Alfa AF: 0.916 Hom.: 9810

Bravo AF: 0.910

Asia WGS AF: 0.952 AC: 3310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.35
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2946831; hg19: chr12-102786780;