rs1115713

Positions:

• chr20-31548187-A-G

Variant summary

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

The NM_178581.3(HM13):​c.455-842A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 692,978 control chromosomes in the GnomAD database, including 11,711 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 0.22 (5964 hom., cov: 32)
  • Exomes 𝑓: 0.12 (5747 hom.)
• Consequence: HM13 NM_178581.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

Genes affected

HM13 (HGNC:16435): (histocompatibility minor 13) The protein encoded by this gene, which localizes to the endoplasmic reticulum, catalyzes intramembrane proteolysis of some signal peptides after they have been cleaved from a preprotein. This activity is required to generate signal sequence-derived human lymphocyte antigen-E epitopes that are recognized by the immune system, and to process hepatitis C virus core protein. The encoded protein is an integral membrane protein with sequence motifs characteristic of the presenilin-type aspartic proteases. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HM13	NM_178581.3	c.455-842A>G		intron_variant		ENST00000398174.9
HM13	NM_030789.4	c.455-842A>G		intron_variant
HM13	NM_178580.3	c.455-842A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HM13	ENST00000398174.9	c.455-842A>G		intron_variant		1	NM_178581.3	A1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34047 AN: 151978 Hom.: 5942 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.194

GnomAD4 exome AF: 0.121 AC: 65675 AN: 540882 Hom.: 5747 AF XY: 0.116 AC XY: 33227 AN XY: 287366

Gnomad4 AFR exome AF: 0.496

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.0996

Gnomad4 EAS exome AF: 0.000115

Gnomad4 SAS exome AF: 0.0400

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.224 AC: 34103 AN: 152096 Hom.: 5964 Cov.: 32 AF XY: 0.222 AC XY: 16472 AN XY: 74348

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0386

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.192

Alfa AF: 0.143 Hom.: 1988

Bravo AF: 0.239

Asia WGS AF: 0.0530 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1115713; hg19: chr20-30135990;