chr12-102368678-T-G

Position:

• chr12-102368678-T-G

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.171094T>G 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 0.0354 in 152,336 control chromosomes in the GnomAD database, including 371 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 (371 hom., cov: 32)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.696+19746T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.171094T>G		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.1066+19746T>G		intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1	n.449+19746T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0353 AC: 5377 AN: 152136 Hom.: 366 Cov.: 32

Gnomad AFR AF: 0.00644

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0430

GnomAD4 exome AF: 0.0122 AC: 1 AN: 82 Hom.: 0 Cov.: 0 AF XY: 0.0161 AC XY: 1 AN XY: 62

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0354 AC: 5390 AN: 152254 Hom.: 371 Cov.: 32 AF XY: 0.0406 AC XY: 3024 AN XY: 74434

Gnomad4 AFR AF: 0.00642

Gnomad4 AMR AF: 0.0999

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.0563

Gnomad4 FIN AF: 0.0792

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0228 Hom.: 19

Bravo AF: 0.0374

Asia WGS AF: 0.188 AC: 650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.92
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1106381; hg19: chr12-102762456;