rs12151195

Variant names:

• chr19-35068302-T-C
• rs12151195
• ENST00000392227.2:n.405-8524A>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.405-8524A>G variant causes a intron 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 ENST00000392227.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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.405-8524A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPN-AS1	ENST00000392227.2	TSL:2	n.405-8524A>G		intron	N/A
	HPN-AS1	ENST00000653822.1		n.213-15183A>G		intron	N/A
	HPN-AS1	ENST00000666194.1		n.193-15183A>G		intron	N/A

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

African (AFR) AF: 0.218 AC: 9043 AN: 41502

American (AMR) AF: 0.0625 AC: 955 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0730 AC: 253 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5186

South Asian (SAS) AF: 0.0748 AC: 360 AN: 4812

European-Finnish (FIN) AF: 0.0701 AC: 744 AN: 10616

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0785 AC: 5339 AN: 67992

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0831 Hom.: 1750

Bravo AF: 0.114

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.54
PhyloP100		0.0040
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12151195; hg19: chr19-35559206;