12-102394036-A-G

Variant names:

• chr12-102394036-A-G
• rs2946834
• ENST00000626826.1:n.196452A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 54 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELLPAR	ENST00000626826.1	TSL:6	n.196452A>G		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000635615.1	TSL:5	n.450-29035A>G		intron	N/A
	LINC02456	ENST00000704346.1		n.1067-29035A>G		intron	N/A

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

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) AF: 0.500 AC: 1 AN: 2

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.714 AC: 10 AN: 14

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.502 AC: 20816 AN: 41472

American (AMR) AF: 0.642 AC: 9798 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2796 AN: 5166

South Asian (SAS) AF: 0.680 AC: 3271 AN: 4808

European-Finnish (FIN) AF: 0.768 AC: 8132 AN: 10588

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46379 AN: 67980

Other (OTH) AF: 0.610 AC: 1286 AN: 2108

Alfa AF: 0.655 Hom.: 73598

Bravo AF: 0.609

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2946834; hg19: chr12-102787814;