19-12913436-A-C

Position:

• chr19-12913436-A-C

Variant summary

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

The ENST00000293695.8(SYCE2):​c.131+4786T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,934 control chromosomes in the GnomAD database, including 30,244 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 0.63 (30244 hom., cov: 32)
• Consequence: SYCE2 ENST00000293695.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

Genes affected

SYCE2 (HGNC:27411): (synaptonemal complex central element protein 2) The protein encoded by this gene is part of the synaptonemal complex formed between homologous chromosomes during meiotic prophase. The encoded protein associates with SYCP1 and SYCE1 and is found only where chromosome cores are synapsed. [provided by RefSeq, Dec 2012]

GCDH (HGNC:4189): (glutaryl-CoA dehydrogenase) The protein encoded by this gene belongs to the acyl-CoA dehydrogenase family. It catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and CO(2) in the degradative pathway of L-lysine, L-hydroxylysine, and L-tryptophan metabolism. It uses electron transfer flavoprotein as its electron acceptor. The enzyme exists in the mitochondrial matrix as a homotetramer of 45-kD subunits. Mutations in this gene result in the metabolic disorder glutaric aciduria type 1, which is also known as glutaric acidemia type I. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 12. [provided by RefSeq, Mar 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYCE2	NM_001105578.2	c.131+4786T>G		intron_variant		ENST00000293695.8	NP_001099048.1
SYCE2	XM_011527882.3	c.131+4786T>G		intron_variant			XP_011526184.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYCE2	ENST00000293695.8	c.131+4786T>G		intron_variant		1	NM_001105578.2	ENSP00000293695	P1
GCDH	ENST00000591050.1	c.211-559A>C		intron_variant		3		ENSP00000467735

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95173 AN: 151816 Hom.: 30220 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.627 AC: 95234 AN: 151934 Hom.: 30244 Cov.: 32 AF XY: 0.633 AC XY: 46968 AN XY: 74246

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.621

Alfa AF: 0.596 Hom.: 5507

Bravo AF: 0.612

Asia WGS AF: 0.736 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.51

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: rs741702; hg19: chr19-13024250;