16-83968768-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_019065.3(NECAB2):​c.120G>T​(p.Glu40Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000127 in 948,426 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

NECAB2
NM_019065.3 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.55
Variant links:
Genes affected
NECAB2 (HGNC:23746): (N-terminal EF-hand calcium binding protein 2) The protein encoded by this gene is a neuronal calcium-binding protein that binds to and modulates the function of at least two receptors, adenosine A(2A) receptor and metabotropic glutamate receptor type 5. [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.030404717).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NECAB2NM_019065.3 linkuse as main transcriptc.120G>T p.Glu40Asp missense_variant 1/13 ENST00000305202.9
NECAB2NM_001329748.1 linkuse as main transcriptc.120G>T p.Glu40Asp missense_variant 1/12
NECAB2NM_001329749.2 linkuse as main transcriptc.-104G>T 5_prime_UTR_variant 1/12
NECAB2XM_047434240.1 linkuse as main transcriptc.-22-3383G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NECAB2ENST00000305202.9 linkuse as main transcriptc.120G>T p.Glu40Asp missense_variant 1/131 NM_019065.3 P1Q7Z6G3-1
NECAB2ENST00000681513.1 linkuse as main transcriptn.525G>T non_coding_transcript_exon_variant 1/13

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.0000127
AC:
12
AN:
948426
Hom.:
0
Cov.:
31
AF XY:
0.0000157
AC XY:
7
AN XY:
445736
show subpopulations
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:
0.0000108
Gnomad4 OTH exome
AF:
0.0000583
GnomAD4 genome
Cov.:
30

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 06, 2024The c.120G>T (p.E40D) alteration is located in exon 1 (coding exon 1) of the NECAB2 gene. This alteration results from a G to T substitution at nucleotide position 120, causing the glutamic acid (E) at amino acid position 40 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
8.6
DANN
Benign
0.96
DEOGEN2
Benign
0.0041
T
Eigen
Benign
-0.98
Eigen_PC
Benign
-0.90
FATHMM_MKL
Benign
0.30
N
LIST_S2
Benign
0.35
T
M_CAP
Benign
0.0089
T
MetaRNN
Benign
0.030
T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.20
N
MutationTaster
Benign
1.0
N
PrimateAI
Pathogenic
0.90
D
PROVEAN
Benign
0.14
N
REVEL
Benign
0.071
Sift
Benign
0.64
T
Sift4G
Benign
0.55
T
Polyphen
0.10
B
Vest4
0.061
MutPred
0.059
Gain of loop (P = 0.0435);
MVP
0.014
ClinPred
0.049
T
GERP RS
-1.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.2
Varity_R
0.052
gMVP
0.17

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-84002373; API