chr16-83968659-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_019065.3(NECAB2):​c.11G>C​(p.Arg4Pro) 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. 13/20 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)

Consequence

NECAB2
NM_019065.3 missense

Scores

1
2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.02
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]

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ACMG classification

Classification made for transcript

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=0.070254445).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NECAB2NM_019065.3 linkuse as main transcriptc.11G>C p.Arg4Pro missense_variant 1/13 ENST00000305202.9
NECAB2NM_001329748.1 linkuse as main transcriptc.11G>C p.Arg4Pro missense_variant 1/12
NECAB2NM_001329749.2 linkuse as main transcriptc.-213G>C 5_prime_UTR_variant 1/12
NECAB2XM_047434240.1 linkuse as main transcriptc.-23+3423G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NECAB2ENST00000305202.9 linkuse as main transcriptc.11G>C p.Arg4Pro missense_variant 1/131 NM_019065.3 P1Q7Z6G3-1
NECAB2ENST00000681513.1 linkuse as main transcriptn.416G>C non_coding_transcript_exon_variant 1/13

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Cov.:
31
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 GeneticsDec 17, 2023The c.11G>C (p.R4P) alteration is located in exon 1 (coding exon 1) of the NECAB2 gene. This alteration results from a G to C substitution at nucleotide position 11, causing the arginine (R) at amino acid position 4 to be replaced by a proline (P). 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
Uncertain
0.38
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
22
DANN
Benign
0.97
DEOGEN2
Benign
0.010
T
Eigen
Benign
-0.51
Eigen_PC
Benign
-0.44
FATHMM_MKL
Benign
0.27
N
LIST_S2
Benign
0.53
T
M_CAP
Benign
0.0088
T
MetaRNN
Benign
0.070
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N
MutationTaster
Benign
0.94
N
PrimateAI
Pathogenic
0.81
D
PROVEAN
Benign
-0.31
N
REVEL
Benign
0.021
Sift
Benign
0.030
D
Sift4G
Uncertain
0.041
D
Polyphen
0.026
B
Vest4
0.22
MutPred
0.27
Loss of MoRF binding (P = 0.0034);
MVP
0.13
ClinPred
0.43
T
GERP RS
1.5
Varity_R
0.28
gMVP
0.46

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: chr16-84002264; API