rs7258700

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-35106825-C-A
• chr19-35106825-C-G
• chr19-35106825-C-T

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>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904701	XR_007067238.1	n.2500C>A		non_coding_transcript_exon_variant	Exon 2 of 3
LOC124904701	XM_047439795.1	c.*907C>A		3_prime_UTR_variant	Exon 2 of 2		XP_047295751.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285526	ENST00000648240.1	c.-284C>A		5_prime_UTR_variant	Exon 1 of 9			ENSP00000497169.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 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: 0.00 AC: 0 AN: 158434

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 8193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.28
DANN	Benign	0.72
PhyloP100		-0.99
PromoterAI		-0.031	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;