12-102241743-C-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.285 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELLPAR	ENST00000626826.1	TSL:6	n.44159C>A		non_coding_transcript_exon	Exon 1 of 1

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

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) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.285 AC: 11810 AN: 41374

American (AMR) AF: 0.214 AC: 3256 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 359 AN: 3458

East Asian (EAS) AF: 0.297 AC: 1528 AN: 5144

South Asian (SAS) AF: 0.0901 AC: 433 AN: 4808

European-Finnish (FIN) AF: 0.114 AC: 1205 AN: 10600

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8408 AN: 67776

Other (OTH) AF: 0.200 AC: 421 AN: 2106

Alfa AF: 0.166 Hom.: 416

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 812 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	0.19
DANN	Benign	0.27
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs12426318; hg19: chr12-102635521;