17-7218550-C-A

Variant names:

• chr17-7218550-C-A
• rs372479041
• ENST00000648172.8:c.109G>T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_001365.5(DLG4):​c.109G>T​(p.Ala37Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000163 in 1,408,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A37T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000016 (0 hom.)
• Consequence: DLG4 NM_001365.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.04

Genes affected

DLG4 (HGNC:2903): (discs large MAGUK scaffold protein 4) This gene encodes a member of the membrane-associated guanylate kinase (MAGUK) family. It heteromultimerizes with another MAGUK protein, DLG2, and is recruited into NMDA receptor and potassium channel clusters. These two MAGUK proteins may interact at postsynaptic sites to form a multimeric scaffold for the clustering of receptors, ion channels, and associated signaling proteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACADVL (HGNC:92): (acyl-CoA dehydrogenase very long chain) The protein encoded by this gene is targeted to the inner mitochondrial membrane where it catalyzes the first step of the mitochondrial fatty acid beta-oxidation pathway. This acyl-Coenzyme A dehydrogenase is specific to long-chain and very-long-chain fatty acids. A deficiency in this gene product reduces myocardial fatty acid beta-oxidation and is associated with cardiomyopathy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.18596801).
• BS2: High AC in GnomAdExome4 at 23 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLG4	NM_001365.5	c.109G>T	p.Ala37Ser	missense_variant	Exon 2 of 22		NP_001356.1
DLG4	NM_001321074.1	c.109G>T	p.Ala37Ser	missense_variant	Exon 2 of 22		NP_001308003.1
ACADVL	NM_001270447.2	c.131+732C>A		intron_variant	Intron 2 of 20		NP_001257376.1
DLG4	NR_135527.1	n.1310G>T		non_coding_transcript_exon_variant	Exon 2 of 21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLG4	ENST00000648172.8	c.109G>T	p.Ala37Ser	missense_variant	Exon 2 of 22			ENSP00000497806.3
DLG4	ENST00000491753.2	n.109G>T		non_coding_transcript_exon_variant	Exon 2 of 21	2		ENSP00000467897.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000596 AC: 1 AN: 167756 Hom.: 0 AF XY: 0.0000112 AC XY: 1 AN XY: 89376

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000146

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000163 AC: 23 AN: 1408266 Hom.: 0 Cov.: 31 AF XY: 0.0000144 AC XY: 10 AN XY: 695424

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000194

Gnomad4 OTH exome AF: 0.0000342

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.27	.;T
Eigen	Benign	0.021
Eigen_PC	Benign	0.16
FATHMM_MKL	Uncertain	0.76	D
LIST_S2	Benign	0.75	T;T
M_CAP	Benign	0.0094	T
MetaRNN	Benign	0.19	T;T
MetaSVM	Benign	-1.1	T
PROVEAN	Benign	-0.40	.;N
REVEL	Benign	0.056
Sift	Pathogenic	0.0	.;D
Sift4G	Benign	0.13	.;T
Polyphen		0.76	P;B
Vest4		0.51
MutPred		0.59		Loss of stability (P = 0.0598);Loss of stability (P = 0.0598);
MVP		0.56
MPC		1.0
ClinPred		0.85	D
GERP RS		4.4
gMVP		0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs372479041; hg19: chr17-7121869;