12-102394036-A-G

Position:

• chr12-102394036-A-G

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.196452A>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 0.628 in 152,074 control chromosomes in the GnomAD database, including 30,514 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 0.63 (30509 hom., cov: 32)
  • Exomes 𝑓: 0.67 (5 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.697-10077A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.196452A>G		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.1067-29035A>G		intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1	n.450-29035A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95495 AN: 151938 Hom.: 30514 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.615

GnomAD4 exome AF: 0.667 AC: 12 AN: 18 Hom.: 5 Cov.: 0 AF XY: 0.688 AC XY: 11 AN XY: 16

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.714

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.628 AC: 95506 AN: 152056 Hom.: 30509 Cov.: 32 AF XY: 0.632 AC XY: 46951 AN XY: 74326

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.610

Alfa AF: 0.670 Hom.: 49106

Bravo AF: 0.609

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2946834; hg19: chr12-102787814;