chr19-35074103-C-T

Position:

• chr19-35074103-C-T

Variant summary

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

The NR_024562.1(HPN-AS1):​n.404+12853G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,146 control chromosomes in the GnomAD database, including 1,670 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 0.14 (1670 hom., cov: 33)
• Consequence: HPN-AS1 NR_024562.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.38

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HPN-AS1	NR_024562.1	n.404+12853G>A		intron_variant, non_coding_transcript_variant
HPN-AS1	NR_024561.1	n.2379G>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HPN-AS1	ENST00000653822.1	n.212+12853G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21478 AN: 152028 Hom.: 1665 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.141 AC: 21515 AN: 152146 Hom.: 1670 Cov.: 33 AF XY: 0.140 AC XY: 10420 AN XY: 74380

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.145

Alfa AF: 0.125 Hom.: 629

Bravo AF: 0.150

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.019
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8103371; hg19: chr19-35565007;