12-102370439-T-G

Variant names:

• chr12-102370439-T-G
• rs2139570
• ENST00000626826.1:n.172855T>G

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.172855T>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 0.545 in 152,028 control chromosomes in the GnomAD database, including 22,988 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 0.54 (22987 hom., cov: 33)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626826.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELLPAR	ENST00000626826.1	TSL:6	n.172855T>G		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000635615.1	TSL:5	n.449+21507T>G		intron	N/A
	LINC02456	ENST00000704346.1		n.1066+21507T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82730 AN: 151904 Hom.: 22959 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.543

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

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: 0.667 AC: 4 AN: 6

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0296732), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.545 AC: 82809 AN: 152022 Hom.: 22987 Cov.: 33 AF XY: 0.543 AC XY: 40380 AN XY: 74310

African (AFR) AF: 0.650 AC: 26921 AN: 41438

American (AMR) AF: 0.472 AC: 7215 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3214 AN: 5176

South Asian (SAS) AF: 0.420 AC: 2023 AN: 4822

European-Finnish (FIN) AF: 0.560 AC: 5906 AN: 10554

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34201 AN: 67958

Other (OTH) AF: 0.547 AC: 1157 AN: 2116

Alfa AF: 0.322 Hom.: 693

Bravo AF: 0.547

Asia WGS AF: 0.574 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.43
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2139570; hg19: chr12-102764217;