chr21-21292126-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004540.5(NCAM2):c.504C>T(p.Asn168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000545 in 1,610,464 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00030 ( 5 hom. )
Consequence
NCAM2
NM_004540.5 synonymous
NM_004540.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.48
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 made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 21-21292126-C-T is Benign according to our data. Variant chr21-21292126-C-T is described in ClinVar as [Benign]. Clinvar id is 3050462.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.48 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCAM2 | NM_004540.5 | c.504C>T | p.Asn168= | synonymous_variant | 5/18 | ENST00000400546.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCAM2 | ENST00000400546.6 | c.504C>T | p.Asn168= | synonymous_variant | 5/18 | 1 | NM_004540.5 | P1 | |
NCAM2 | ENST00000284894.8 | c.450C>T | p.Asn150= | synonymous_variant | 4/17 | 5 | |||
NCAM2 | ENST00000461281.1 | n.98C>T | non_coding_transcript_exon_variant | 2/5 | 3 | ||||
NCAM2 | ENST00000486367.1 | n.519C>T | non_coding_transcript_exon_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00291 AC: 442AN: 151794Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000797 AC: 197AN: 247104Hom.: 1 AF XY: 0.000537 AC XY: 72AN XY: 134044
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GnomAD4 exome AF: 0.000300 AC: 437AN: 1458552Hom.: 5 Cov.: 30 AF XY: 0.000223 AC XY: 162AN XY: 725546
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NCAM2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 02, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at