rs17439974

chr12-102275055-T-A

Variant summary

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

The ENST00000626826.1(HELLPAR):n.77471T>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 0.287 in 151,918 control chromosomes in the GnomAD database, including 6,470 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 0.29 (6470 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HELLPAR	ENST00000626826.1	n.77471T>A		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.170-531T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43531 AN: 151800 Hom.: 6453 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.309

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.287 AC: 43583 AN: 151918 Hom.: 6470 Cov.: 32 AF XY: 0.287 AC XY: 21303 AN XY: 74290

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.314

Alfa AF: 0.291 Hom.: 799

Bravo AF: 0.287

Asia WGS AF: 0.377 AC: 1297 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.5
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17439974; hg19: chr12-102668833;