rs4503597

Variant names:

• chr12-102260794-G-A
• rs4503597
• ENST00000626826.1:n.63210G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-102260794-G-A
• chr12-102260794-G-C
• chr12-102260794-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626826.1(HELLPAR):​n.63210G>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 0.564 in 151,974 control chromosomes in the GnomAD database, including 25,051 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 0.56 (25050 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

Genes affected

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

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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.63210G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02456	ENST00000704346.1	n.104-1291G>A		intron_variant	Intron 1 of 10

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85617 AN: 151850 Hom.: 24990 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.553

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.564 AC: 85740 AN: 151968 Hom.: 25050 Cov.: 32 AF XY: 0.563 AC XY: 41831 AN XY: 74262

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.556

Alfa AF: 0.484 Hom.: 3587

Bravo AF: 0.569

Asia WGS AF: 0.568 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4503597; hg19: chr12-102654572;