rs17439974

Variant names:

• chr12-102275055-T-A
• rs17439974
• ENST00000626826.1:n.77471T>A

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.77471T>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 0.287 in 151,918 control chromosomes in the GnomAD database, including 6,470 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 0.29 (6470 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.77471T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02456	ENST00000704346.1	n.170-531T>A		intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43531 AN: 151800 Hom.: 6453 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.309

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.287 AC: 43583 AN: 151918 Hom.: 6470 Cov.: 32 AF XY: 0.287 AC XY: 21303 AN XY: 74290

African (AFR) AF: 0.237 AC: 9841 AN: 41508

American (AMR) AF: 0.294 AC: 4495 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2196 AN: 5176

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4812

European-Finnish (FIN) AF: 0.319 AC: 3350 AN: 10514

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20788 AN: 67854

Other (OTH) AF: 0.314 AC: 664 AN: 2114

Alfa AF: 0.291 Hom.: 799

Bravo AF: 0.287

Asia WGS AF: 0.377 AC: 1297 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs17439974; hg19: chr12-102668833;