ENST00000626826.1:n.176530G>A

Variant names:

• chr12-102374114-G-A
• rs1980236
• ENST00000626826.1:n.176530G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626826.1(HELLPAR):​n.176530G>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 0.564 in 152,030 control chromosomes in the GnomAD database, including 25,132 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 (25132 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626826.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELLPAR	ENST00000626826.1	TSL:6	n.176530G>A		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000635615.1	TSL:5	n.449+25182G>A		intron	N/A
	LINC02456	ENST00000704346.1		n.1066+25182G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85601 AN: 151908 Hom.: 25073 Cov.: 33

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.555

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.556

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.564 AC: 85728 AN: 152026 Hom.: 25132 Cov.: 33 AF XY: 0.563 AC XY: 41826 AN XY: 74294

African (AFR) AF: 0.736 AC: 30536 AN: 41494

American (AMR) AF: 0.484 AC: 7404 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3192 AN: 5164

South Asian (SAS) AF: 0.417 AC: 2011 AN: 4826

European-Finnish (FIN) AF: 0.547 AC: 5775 AN: 10562

Middle Eastern (MID) AF: 0.569 AC: 164 AN: 288

European-Non Finnish (NFE) AF: 0.493 AC: 33462 AN: 67914

Other (OTH) AF: 0.559 AC: 1181 AN: 2112

Alfa AF: 0.507 Hom.: 14593

Bravo AF: 0.571

Asia WGS AF: 0.578 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.052
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1980236; hg19: chr12-102767892;