rs1996656

Variant names:

• chr12-102358184-A-G
• rs1996656
• ENST00000626826.1:n.160600A>G

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.160600A>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 0.154 in 152,174 control chromosomes in the GnomAD database, including 1,907 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 0.15 (1907 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763
• Publications: 15 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 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.160600A>G		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000635615.1	TSL:5	n.449+9252A>G		intron	N/A
	LINC02456	ENST00000704346.1		n.1066+9252A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23360 AN: 152054 Hom.: 1904 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.154 AC: 23372 AN: 152172 Hom.: 1907 Cov.: 32 AF XY: 0.152 AC XY: 11302 AN XY: 74392

African (AFR) AF: 0.111 AC: 4615 AN: 41540

American (AMR) AF: 0.0996 AC: 1522 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 543 AN: 3470

East Asian (EAS) AF: 0.171 AC: 884 AN: 5168

South Asian (SAS) AF: 0.153 AC: 738 AN: 4826

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10586

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12500 AN: 67988

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.169 Hom.: 289

Bravo AF: 0.143

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.2
DANN	Benign	0.84
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1996656; hg19: chr12-102751962;