ENST00000392227.2:n.405-8792A>G

Variant names:

• chr19-35068570-T-C
• rs11671010
• ENST00000392227.2:n.405-8792A>G

Variant summary

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

The ENST00000392227.2(HPN-AS1):​n.405-8792A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,176 control chromosomes in the GnomAD database, including 1,274 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 0.11 (1274 hom., cov: 32)
• Consequence: HPN-AS1 ENST00000392227.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 10 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392227.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPN-AS1	NR_024562.1		n.405-8792A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPN-AS1	ENST00000392227.2	TSL:2	n.405-8792A>G		intron	N/A
	HPN-AS1	ENST00000653822.1		n.213-15451A>G		intron	N/A
	HPN-AS1	ENST00000666194.1		n.193-15451A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16622 AN: 152058 Hom.: 1274 Cov.: 32

Gnomad AFR AF: 0.0296

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.0889

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.109 AC: 16620 AN: 152176 Hom.: 1274 Cov.: 32 AF XY: 0.108 AC XY: 8047 AN XY: 74394

African (AFR) AF: 0.0295 AC: 1225 AN: 41530

American (AMR) AF: 0.0785 AC: 1200 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3470

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5180

South Asian (SAS) AF: 0.0946 AC: 456 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1903 AN: 10574

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11090 AN: 67998

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.142 Hom.: 5580

Bravo AF: 0.0993

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.9
DANN	Benign	0.70
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11671010;

hg19: chr19-35559474;