chr3-123121029-G-A

Variant names:

• chr3-123121029-G-A
• rs3792366
• NM_006810.4:c.610-3037G>A

Variant summary

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

The NM_006810.4(PDIA5):​c.610-3037G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,060 control chromosomes in the GnomAD database, including 21,707 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 0.52 (21707 hom., cov: 32)
• Consequence: PDIA5 NM_006810.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 17 publications found

Genes affected

PDIA5 (HGNC:24811): (protein disulfide isomerase family A member 5) This gene encodes a member of the disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins that catalyze protein folding and thiol-disulfide interchange reactions. The encoded protein has an N-terminal ER-signal sequence, three catalytically active thioredoxin (TRX) domains, a TRX-like domain, and a C-terminal ER-retention sequence. The N-terminal TRX-like domain is the primary binding site for the major ER chaperone calreticulin and possibly other proteins and substrates as well. Alternative splicing results in multiple protein- and non-protein-coding transcript variants. [provided by RefSeq, Dec 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDIA5	NM_006810.4	c.610-3037G>A		intron_variant	Intron 8 of 16	ENST00000316218.12	NP_006801.1
PDIA5	NR_028444.2	n.750-3037G>A		intron_variant	Intron 8 of 15
PDIA5	XR_007095629.1	n.750-3037G>A		intron_variant	Intron 8 of 13
PDIA5	XR_007095630.1	n.750-3037G>A		intron_variant	Intron 8 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDIA5	ENST00000316218.12	c.610-3037G>A		intron_variant	Intron 8 of 16	1	NM_006810.4	ENSP00000323313.7
PDIA5	ENST00000489923.5	n.610-3037G>A		intron_variant	Intron 8 of 15	1		ENSP00000417520.1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79778 AN: 151942 Hom.: 21704 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.525 AC: 79805 AN: 152060 Hom.: 21707 Cov.: 32 AF XY: 0.527 AC XY: 39172 AN XY: 74344

African (AFR) AF: 0.374 AC: 15481 AN: 41448

American (AMR) AF: 0.587 AC: 8975 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2230 AN: 5174

South Asian (SAS) AF: 0.517 AC: 2488 AN: 4816

European-Finnish (FIN) AF: 0.626 AC: 6618 AN: 10564

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40360 AN: 67976

Other (OTH) AF: 0.543 AC: 1147 AN: 2114

Alfa AF: 0.549 Hom.: 36665

Bravo AF: 0.513

Asia WGS AF: 0.483 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.70
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3792366; hg19: chr3-122839876;