rs1607693

chr12-102336290-G-A

Variant summary

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

The ENST00000626826.1(HELLPAR):n.138706G>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 0.0352 in 152,246 control chromosomes in the GnomAD database, including 364 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 0.035 (364 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.647-12593G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HELLPAR	ENST00000626826.1	n.138706G>A		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.1017-12593G>A		intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1	n.400-12593G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5343 AN: 152098 Hom.: 359 Cov.: 32

Gnomad AFR AF: 0.00644

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0430

GnomAD4 exome AF: 0.100 AC: 3 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3 AN XY: 22

Gnomad4 NFE exome AF: 0.0769

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.0352 AC: 5356 AN: 152216 Hom.: 364 Cov.: 32 AF XY: 0.0404 AC XY: 3006 AN XY: 74440

Gnomad4 AFR AF: 0.00643

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.0566

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0227 Hom.: 17

Bravo AF: 0.0372

Asia WGS AF: 0.186 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.7
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1607693; hg19: chr12-102730068;