NM_004540.5:c.56-134799G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004540.5(NCAM2):c.56-134799G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,022 control chromosomes in the GnomAD database, including 5,216 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5216 hom., cov: 33)
Consequence
NCAM2
NM_004540.5 intron
NM_004540.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.112
Publications
0 publications found
Genes affected
NCAM2 (HGNC:7657): (neural cell adhesion molecule 2) The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membrane protein and may function in selective fasciculation and zone-to-zone projection of the primary olfactory axons. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.248 AC: 37682AN: 151902Hom.: 5214 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
37682
AN:
151902
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.248 AC: 37679AN: 152022Hom.: 5216 Cov.: 33 AF XY: 0.255 AC XY: 18940AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
37679
AN:
152022
Hom.:
Cov.:
33
AF XY:
AC XY:
18940
AN XY:
74300
show subpopulations
African (AFR)
AF:
AC:
5754
AN:
41486
American (AMR)
AF:
AC:
4291
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
1083
AN:
3468
East Asian (EAS)
AF:
AC:
2351
AN:
5178
South Asian (SAS)
AF:
AC:
1735
AN:
4818
European-Finnish (FIN)
AF:
AC:
3065
AN:
10554
Middle Eastern (MID)
AF:
AC:
94
AN:
294
European-Non Finnish (NFE)
AF:
AC:
18345
AN:
67938
Other (OTH)
AF:
AC:
576
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1403
2806
4208
5611
7014
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
404
808
1212
1616
2020
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1278
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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