chr12-102241743-C-A

Variant names:

• chr12-102241743-C-A
• rs12426318
• ENST00000626826.1:n.44159C>A

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.44159C>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 0.182 in 151,692 control chromosomes in the GnomAD database, including 2,928 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 0.18 (2928 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

HELLPAR (HGNC:43984): (HELLP associated long non-coding RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.44159C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27538 AN: 151566 Hom.: 2901 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.182 AC: 27618 AN: 151684 Hom.: 2928 Cov.: 32 AF XY: 0.183 AC XY: 13539 AN XY: 74150

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.0901

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.200

Alfa AF: 0.163 Hom.: 391

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12426318; hg19: chr12-102635521;