ENST00000626826.1:n.194710G>T

Variant names:

• chr12-102392294-G-T
• rs10860862
• ENST00000626826.1:n.194710G>T

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.194710G>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 0.215 in 152,096 control chromosomes in the GnomAD database, including 3,785 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 0.22 (3785 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.697-11819G>T		intron_variant	Intron 6 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.194710G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02456	ENST00000635615.1	n.450-30777G>T		intron_variant	Intron 4 of 5	5
LINC02456	ENST00000704346.1	n.1067-30777G>T		intron_variant	Intron 9 of 10

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32697 AN: 151954 Hom.: 3775 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.200

GnomAD4 exome AF: 0.333 AC: 8 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.389 AC XY: 7 AN XY: 18

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.333 AC: 6 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.215 AC: 32744 AN: 152072 Hom.: 3785 Cov.: 32 AF XY: 0.215 AC XY: 15980 AN XY: 74330

African (AFR) AF: 0.297 AC: 12325 AN: 41468

American (AMR) AF: 0.162 AC: 2474 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3468

East Asian (EAS) AF: 0.165 AC: 856 AN: 5180

South Asian (SAS) AF: 0.165 AC: 794 AN: 4816

European-Finnish (FIN) AF: 0.242 AC: 2557 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12415 AN: 67974

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.182 Hom.: 4518

Bravo AF: 0.213

Asia WGS AF: 0.171 AC: 594 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
DANN	Benign	0.69
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10860862; hg19: chr12-102786072; COSMIC: COSV61706368;