21-20998610-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004540.5(NCAM2):c.47G>A(p.Ser16Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000123 in 1,461,798 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S16S) has been classified as Likely benign.
Frequency
Consequence
NM_004540.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCAM2 | NM_004540.5 | c.47G>A | p.Ser16Asn | missense_variant | 1/18 | ENST00000400546.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCAM2 | ENST00000400546.6 | c.47G>A | p.Ser16Asn | missense_variant | 1/18 | 1 | NM_004540.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246890Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134180
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461798Hom.: 1 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727204
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.47G>A (p.S16N) alteration is located in exon 1 (coding exon 1) of the NCAM2 gene. This alteration results from a G to A substitution at nucleotide position 47, causing the serine (S) at amino acid position 16 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at