3-175097135-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_207015.3(NAALADL2):c.389G>T(p.Cys130Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,506 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C130Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_207015.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAALADL2 | NM_207015.3 | c.389G>T | p.Cys130Phe | missense_variant | 2/14 | ENST00000454872.6 | |
NAALADL2-AS3 | NR_046390.1 | n.110+15409C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAALADL2 | ENST00000454872.6 | c.389G>T | p.Cys130Phe | missense_variant | 2/14 | 1 | NM_207015.3 | P1 | |
NAALADL2-AS3 | ENST00000453180.5 | n.110+15409C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248782Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134946
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461506Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727046
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.389G>T (p.C130F) alteration is located in exon 2 (coding exon 2) of the NAALADL2 gene. This alteration results from a G to T substitution at nucleotide position 389, causing the cysteine (C) at amino acid position 130 to be replaced by a phenylalanine (F). 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