11-34915816-C-T

Variant names:

• chr11-34915816-C-T
• rs3763932
• NM_015957.4:c.57+412G>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_015957.4(APIP):​c.57+412G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 236,070 control chromosomes in the GnomAD database, including 4,595 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.19 (3886 hom., cov: 32)
  • Exomes 𝑓: 0.11 (709 hom.)
• Consequence: APIP NM_015957.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.854

Genes affected

APIP (HGNC:17581): (APAF1 interacting protein) Enables identical protein binding activity; methylthioribulose 1-phosphate dehydratase activity; and zinc ion binding activity. Involved in several processes, including L-methionine salvage from methylthioadenosine; protein homotetramerization; and pyroptosis. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PDHX (HGNC:21350): (pyruvate dehydrogenase complex component X) The pyruvate dehydrogenase (PDH) complex is located in the mitochondrial matrix and catalyzes the conversion of pyruvate to acetyl coenzyme A. The PDH complex thereby links glycolysis to Krebs cycle. The PDH complex contains three catalytic subunits, E1, E2, and E3, two regulatory subunits, E1 kinase and E1 phosphatase, and a non-catalytic subunit, E3 binding protein (E3BP). This gene encodes the E3 binding protein subunit; also known as component X of the pyruvate dehydrogenase complex. This protein tethers E3 dimers to the E2 core of the PDH complex. Defects in this gene are a cause of pyruvate dehydrogenase deficiency which results in neurological dysfunction and lactic acidosis in infancy and early childhood. This protein is also a minor antigen for antimitochondrial antibodies. These autoantibodies are present in nearly 95% of patients with the autoimmune liver disease primary biliary cirrhosis (PBC). In PBC, activated T lymphocytes attack and destroy epithelial cells in the bile duct where this protein is abnormally distributed and overexpressed. PBC eventually leads to cirrhosis and liver failure. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-34915816-C-T is Benign according to our data. Variant chr11-34915816-C-T is described in ClinVar as [Benign]. Clinvar id is 683416.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APIP	NM_015957.4	c.57+412G>A		intron_variant	Intron 1 of 6	ENST00000395787.4	NP_057041.2
APIP	XM_011520154.4	c.13+412G>A		intron_variant	Intron 1 of 7		XP_011518456.1
APIP	XM_017017875.3	c.-301+412G>A		intron_variant	Intron 1 of 7		XP_016873364.1
PDHX	XM_011520390.2	c.-143C>T		upstream_gene_variant			XP_011518692.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APIP	ENST00000395787.4	c.57+412G>A		intron_variant	Intron 1 of 6	1	NM_015957.4	ENSP00000379133.3
APIP	ENST00000527830.1	n.124+412G>A		intron_variant	Intron 1 of 5	2
PDHX	ENST00000533550.5	c.-143C>T		upstream_gene_variant		4		ENSP00000431281.1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28740 AN: 152042 Hom.: 3879 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.179

GnomAD4 exome AF: 0.112 AC: 9415 AN: 83910 Hom.: 709 Cov.: 0 AF XY: 0.113 AC XY: 4851 AN XY: 43000

Gnomad4 AFR exome AF: 0.368

Gnomad4 AMR exome AF: 0.0942

Gnomad4 ASJ exome AF: 0.140

Gnomad4 EAS exome AF: 0.0961

Gnomad4 SAS exome AF: 0.108

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.123

GnomAD4 genome AF: 0.189 AC: 28781 AN: 152160 Hom.: 3886 Cov.: 32 AF XY: 0.186 AC XY: 13850 AN XY: 74396

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0869

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.177

Alfa AF: 0.157 Hom.: 340

Bravo AF: 0.199

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.81

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: rs3763932; hg19: chr11-34937363;