ENST00000648240.1:c.-284C>G

Variant names:

• chr19-35106825-C-G
• rs7258700
• ENST00000648240.1:c.-284C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000648240.1(ENSG00000285526):​c.-284C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000033 in 303,348 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000033 (0 hom.)
• Consequence: ENSG00000285526 ENST00000648240.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 5 publications found

Genes affected

ENSG00000285526 (HGNC:):

HPN-AS1 (HGNC:47041): (HPN antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.028).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648240.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285526	ENST00000648240.1		c.-284C>G		5_prime_UTR	Exon 1 of 9	ENSP00000497169.1
	ENSG00000179066	ENST00000313865.6	TSL:6	n.857C>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000179066	ENST00000616460.2	TSL:6	n.857C>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000780 AC: 1 AN: 128242 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000210

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000330 AC: 1 AN: 303348 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 172686

African (AFR) AF: 0.00 AC: 0 AN: 8582

American (AMR) AF: 0.00 AC: 0 AN: 27268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10774

East Asian (EAS) AF: 0.00 AC: 0 AN: 9202

South Asian (SAS) AF: 0.00 AC: 0 AN: 59736

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12366

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2780

European-Non Finnish (NFE) AF: 0.00000631 AC: 1 AN: 158434

Other (OTH) AF: 0.00 AC: 0 AN: 14206

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000109 Hom.: 8193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.37
DANN	Benign	0.82
PhyloP100		-0.99
PromoterAI		0.035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7258700; hg19: chr19-35597729;