rs12151195

Positions:

• chr19-35068302-T-C

Variant summary

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

The NR_024562.1(HPN-AS1):​n.405-8524A>G 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 0.111 in 152,172 control chromosomes in the GnomAD database, including 1,301 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 (1301 hom., cov: 32)
• Consequence: HPN-AS1 NR_024562.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HPN-AS1	NR_024562.1	n.405-8524A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HPN-AS1	ENST00000653822.1	n.213-15183A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16919 AN: 152054 Hom.: 1297 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0750

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.111 AC: 16951 AN: 152172 Hom.: 1301 Cov.: 32 AF XY: 0.107 AC XY: 7988 AN XY: 74400

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.0730

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0748

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.0794 Hom.: 1088

Bravo AF: 0.114

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12151195; hg19: chr19-35559206;