chr3-175234070-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207015.3(NAALADL2):āc.685A>Gā(p.Ser229Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_207015.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAALADL2 | NM_207015.3 | c.685A>G | p.Ser229Gly | missense_variant | 3/14 | ENST00000454872.6 | NP_996898.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAALADL2 | ENST00000454872.6 | c.685A>G | p.Ser229Gly | missense_variant | 3/14 | 1 | NM_207015.3 | ENSP00000404705 | P1 | |
NAALADL2 | ENST00000485853.5 | n.771A>G | non_coding_transcript_exon_variant | 3/4 | 1 | |||||
NAALADL2 | ENST00000473253.5 | n.917A>G | non_coding_transcript_exon_variant | 3/11 | 2 | |||||
NAALADL2 | ENST00000489299.5 | n.424A>G | non_coding_transcript_exon_variant | 3/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248814Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134952
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461642Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727100
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.685A>G (p.S229G) alteration is located in exon 3 (coding exon 3) of the NAALADL2 gene. This alteration results from a A to G substitution at nucleotide position 685, causing the serine (S) at amino acid position 229 to be replaced by a glycine (G). 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