rs1529191

Positions:

• chr9-100083626-G-A
• chr9-100083626-G-C
• chr9-100083626-G-T

Variant summary

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

The NM_015051.3(ERP44):​c.57+15158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,978 control chromosomes in the GnomAD database, including 17,248 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 0.46 (17248 hom., cov: 32)
• Consequence: ERP44 NM_015051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

ERP44 (HGNC:18311): (endoplasmic reticulum protein 44) This gene encodes a member of the protein disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins. It has an inferred N-terminal signal peptide, a catalytically active thioredoxin (TRX) domain, two TRX-like domains and a C-terminal ER-retention sequence. This protein functions as a pH-regulated chaperone of the secretory pathway and likely plays a role in protein quality control at the endoplasmic reticulum - Golgi interface. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERP44	NM_015051.3	c.57+15158C>T		intron_variant		ENST00000262455.7	NP_055866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERP44	ENST00000262455.7	c.57+15158C>T		intron_variant		1	NM_015051.3	ENSP00000262455	P1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69248 AN: 151860 Hom.: 17247 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.456 AC: 69264 AN: 151978 Hom.: 17248 Cov.: 32 AF XY: 0.465 AC XY: 34568 AN XY: 74316

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.485

Alfa AF: 0.462 Hom.: 3485

Bravo AF: 0.462

Asia WGS AF: 0.745 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	17
DANN	Benign	0.60

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: rs1529191; hg19: chr9-102845908;