rs8103371

Variant names:

• chr19-35074103-C-T
• rs8103371
• NR_024561.1:n.2379G>A

Variant summary

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

The NR_024561.1(HPN-AS1):​n.2379G>A variant causes a non coding transcript exon 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_024561.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.38
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_024561.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPN-AS1	NR_024561.1		n.2379G>A		non_coding_transcript_exon	Exon 4 of 4
	HPN-AS1	NR_024562.1		n.404+12853G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPN-AS1	ENST00000392227.2	TSL:2	n.404+12853G>A		intron	N/A
	HPN-AS1	ENST00000653822.1		n.212+12853G>A		intron	N/A
	HPN-AS1	ENST00000666194.1		n.192+12853G>A		intron	N/A

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

African (AFR) AF: 0.186 AC: 7736 AN: 41512

American (AMR) AF: 0.184 AC: 2814 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3468

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5156

South Asian (SAS) AF: 0.0766 AC: 369 AN: 4818

European-Finnish (FIN) AF: 0.123 AC: 1300 AN: 10610

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8599 AN: 67978

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.125 Hom.: 685

Bravo AF: 0.150

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.019
DANN	Benign	0.42
PhyloP100		-5.4

Splicing

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

Other links and lift over

dbSNP: rs8103371; hg19: chr19-35565007;