18-34755991-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001386795.1(DTNA):c.15T>A(p.Ser5Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S5S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DTNA NM_001386795.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.522

Genes affected

DTNA (HGNC:3057): (dystrobrevin alpha) The protein encoded by this gene belongs to the dystrobrevin subfamily of the dystrophin family. This protein is a component of the dystrophin-associated protein complex (DPC), which consists of dystrophin and several integral and peripheral membrane proteins, including dystroglycans, sarcoglycans, syntrophins and alpha- and beta-dystrobrevin. The DPC localizes to the sarcolemma and its disruption is associated with various forms of muscular dystrophy. Mutations in this gene are associated with left ventricular noncompaction with congenital heart defects. Multiple alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14112571).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DTNA	NM_001386795.1	c.15T>A	p.Ser5Arg	missense_variant	2/23	ENST00000444659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DTNA	ENST00000444659.6	c.15T>A	p.Ser5Arg	missense_variant	2/23	5	NM_001386795.1	P3
	ENST00000596954.1	n.314-356A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Left ventricular noncompaction 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Jun 15, 2022

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with DTNA-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 5 of the DTNA protein (p.Ser5Arg). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
Cadd	Benign	19
Dann	Uncertain	0.99
Eigen	Benign	-0.34
Eigen_PC	Benign	-0.13
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Uncertain	0.93	D;D;D;D;D;D;D;.;D;D;D;D;.;D;D;D;.
M_CAP	Benign	0.0082	T
MetaRNN	Benign	0.14	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.050	N;N;N;.;.;.;N;.;N;N;N;N;N;N;N;N;N
MutationTaster	Benign	0.89	D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.72	T
PROVEAN	Benign	-1.8	N;.;N;.;.;.;.;.;N;N;.;.;.;N;.;N;N
REVEL	Benign	0.11
Sift	Benign	0.050	D;.;T;.;.;.;.;.;T;T;.;.;.;D;.;T;T
Sift4G	Benign	0.40	T;T;T;T;T;T;T;.;T;T;T;T;T;T;T;T;T
Polyphen		0.0	B;.;B;.;.;.;.;.;.;.;.;B;B;B;.;B;B
Vest4		0.35
MutPred		0.22		Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);Loss of phosphorylation at K5 (P = 0.0121);
MVP		0.45
MPC		0.36
ClinPred		0.46	T
GERP RS		3.5
Varity_R		0.15
gMVP		0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-32335955;