rs1607693

Variant names:

• chr12-102336290-G-A
• rs1607693
• ENST00000626826.1:n.138706G>A

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.138706G>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 0.0352 in 152,246 control chromosomes in the GnomAD database, including 364 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 (364 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• 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)

ENSG00000302996 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.647-12593G>A		intron_variant	Intron 5 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.138706G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02456	ENST00000635615.1	n.400-12593G>A		intron_variant	Intron 3 of 5	5
LINC02456	ENST00000704346.1	n.1017-12593G>A		intron_variant	Intron 8 of 10
ENSG00000302996	ENST00000790914.1	n.257-9019C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5343 AN: 152098 Hom.: 359 Cov.: 32

Gnomad AFR AF: 0.00644

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0430

GnomAD4 exome AF: 0.100 AC: 3 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3 AN XY: 22

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: 0.0769 AC: 2 AN: 26

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.0352 AC: 5356 AN: 152216 Hom.: 364 Cov.: 32 AF XY: 0.0404 AC XY: 3006 AN XY: 74440

African (AFR) AF: 0.00643 AC: 267 AN: 41552

American (AMR) AF: 0.0997 AC: 1525 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1431 AN: 5164

South Asian (SAS) AF: 0.0566 AC: 273 AN: 4822

European-Finnish (FIN) AF: 0.0787 AC: 834 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0136 AC: 922 AN: 67994

Other (OTH) AF: 0.0430 AC: 91 AN: 2116

Alfa AF: 0.0227 Hom.: 17

Bravo AF: 0.0372

Asia WGS AF: 0.186 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1607693; hg19: chr12-102730068;