chr19-35068570-T-C

Position:

• chr19-35068570-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

HPN-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HPN-AS1	NR_024562.1	n.405-8792A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HPN-AS1	ENST00000392227.2	n.405-8792A>G		intron_variant		2
HPN-AS1	ENST00000653822.1	n.213-15451A>G		intron_variant
HPN-AS1	ENST00000666194.1	n.193-15451A>G		intron_variant

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

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.148 Hom.: 2421

Bravo AF: 0.0993

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11671010; hg19: chr19-35559474;