12-102384996-C-T

Variant names:

• chr12-102384996-C-T
• rs2139573
• ENST00000626826.1:n.187412C>T

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.187412C>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 0.557 in 151,722 control chromosomes in the GnomAD database, including 24,104 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 0.56 (24100 hom., cov: 30)
  • Exomes 𝑓: 0.69 (4 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.697-19117C>T		intron_variant	Intron 6 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.187412C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02456	ENST00000635615.1	n.449+36064C>T		intron_variant	Intron 4 of 5	5
LINC02456	ENST00000704346.1	n.1066+36064C>T		intron_variant	Intron 9 of 10

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84396 AN: 151588 Hom.: 24058 Cov.: 30

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.551

GnomAD4 exome AF: 0.688 AC: 11 AN: 16 Hom.: 4 Cov.: 0 AF XY: 0.750 AC XY: 9 AN XY: 12

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.625 AC: 5 AN: 8

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.557 AC: 84505 AN: 151706 Hom.: 24100 Cov.: 30 AF XY: 0.558 AC XY: 41350 AN XY: 74170

African (AFR) AF: 0.673 AC: 27813 AN: 41346

American (AMR) AF: 0.479 AC: 7292 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3471 AN: 5134

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4818

European-Finnish (FIN) AF: 0.595 AC: 6281 AN: 10560

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34366 AN: 67842

Other (OTH) AF: 0.555 AC: 1168 AN: 2106

Alfa AF: 0.524 Hom.: 26609

Bravo AF: 0.559

Asia WGS AF: 0.592 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.70
DANN	Benign	0.60
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2139573; hg19: chr12-102778774;