chr13-34942836-C-T

Variant names:

• chr13-34942836-C-T
• rs2059070228
• NM_001385012.1:c.16C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001385012.1(NBEA):​c.16C>T​(p.Pro6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000826 in 1,210,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P6Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 8.3e-7 (0 hom.)
• Consequence: NBEA NM_001385012.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.25

Genes affected

NBEA (HGNC:7648): (neurobeachin) This gene encodes a member of a large, diverse group of A-kinase anchor proteins that target the activity of protein kinase A to specific subcellular sites by binding to its type II regulatory subunits. Brain-specific expression and coat protein-like membrane recruitment of a highly similar protein in mouse suggest an involvement in neuronal post-Golgi membrane traffic. Mutations in this gene may be associated with a form of autism. This gene and its expression are frequently disrupted in patients with multiple myeloma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants may exist, but their full-length nature has not been determined.[provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13100499).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NBEA	NM_001385012.1	c.16C>T	p.Pro6Ser	missense_variant	Exon 1 of 59	ENST00000379939.7	NP_001371941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NBEA	ENST00000379939.7	c.16C>T	p.Pro6Ser	missense_variant	Exon 1 of 59	5	NM_001385012.1	ENSP00000369271.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 8.26e-7 AC: 1 AN: 1210054 Hom.: 0 Cov.: 25 AF XY: 0.00000170 AC XY: 1 AN XY: 587494

African (AFR) AF: 0.00 AC: 0 AN: 23188

American (AMR) AF: 0.00 AC: 0 AN: 12690

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16822

East Asian (EAS) AF: 0.00 AC: 0 AN: 28556

South Asian (SAS) AF: 0.00 AC: 0 AN: 56696

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32550

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3396

European-Non Finnish (NFE) AF: 0.00000101 AC: 1 AN: 986210

Other (OTH) AF: 0.00 AC: 0 AN: 49946

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Neurodevelopmental disorder with or without early-onset generalized epilepsy Uncertain:1

Feb 04, 2022

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.095	T;.;T;.
Eigen	Benign	-0.58
Eigen_PC	Benign	-0.49
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.77	T;T;T;T
M_CAP	Pathogenic	0.43	D
MetaRNN	Benign	0.13	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.69	N;.;.;.
PhyloP100		1.3
PrimateAI	Pathogenic	0.90	D
PROVEAN	Benign	-1.1	N;N;.;N
REVEL	Benign	0.083
Sift	Pathogenic	0.0	D;D;.;D
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		0.014	.;.;.;B
Vest4		0.050
MutPred		0.18		Gain of glycosylation at P6 (P = 0.0149);Gain of glycosylation at P6 (P = 0.0149);Gain of glycosylation at P6 (P = 0.0149);Gain of glycosylation at P6 (P = 0.0149);
MVP		0.16
MPC		0.92
ClinPred		0.41	T
GERP RS		2.4
Varity_R		0.22
gMVP		0.60
Mutation Taster		=86/14	polymorphism

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

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Other links and lift over

dbSNP: rs2059070228; hg19: chr13-35516973;