rs10860860

Positions:

• chr12-102387055-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000626826.1(HELLPAR):​n.189471A>T 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 0.277 in 151,918 control chromosomes in the GnomAD database, including 6,078 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 0.28 (6078 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.697-17058A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.189471A>T		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.1067-36016A>T		intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1	n.450-36016A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42094 AN: 151800 Hom.: 6073 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.283

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: 0.277 AC: 42122 AN: 151918 Hom.: 6078 Cov.: 31 AF XY: 0.272 AC XY: 20177 AN XY: 74244

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.283

Alfa AF: 0.291 Hom.: 782

Bravo AF: 0.278

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	1.6
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10860860; hg19: chr12-102780833;