ENST00000626826.1:n.63210G>A

Variant names:

• chr12-102260794-G-A
• rs4503597
• ENST00000626826.1:n.63210G>A

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.63210G>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 151,974 control chromosomes in the GnomAD database, including 25,051 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 (25050 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELLPAR	ENST00000626826.1	TSL:6	n.63210G>A		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000704346.1		n.104-1291G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85617 AN: 151850 Hom.: 24990 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.553

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

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: 3 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.564 AC: 85740 AN: 151968 Hom.: 25050 Cov.: 32 AF XY: 0.563 AC XY: 41831 AN XY: 74262

African (AFR) AF: 0.725 AC: 30075 AN: 41466

American (AMR) AF: 0.481 AC: 7360 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3470

East Asian (EAS) AF: 0.603 AC: 3114 AN: 5160

South Asian (SAS) AF: 0.414 AC: 1989 AN: 4806

European-Finnish (FIN) AF: 0.564 AC: 5942 AN: 10534

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33891 AN: 67930

Other (OTH) AF: 0.556 AC: 1173 AN: 2108

Alfa AF: 0.549 Hom.: 10810

Bravo AF: 0.569

Asia WGS AF: 0.568 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.25
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4503597; hg19: chr12-102654572;