3-175357320-G-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_207015.3(NAALADL2):c.1090+32995G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,934 control chromosomes in the GnomAD database, including 6,348 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 0.28 ( 6348 hom., cov: 32)
Consequence
NAALADL2
NM_207015.3 intron
NM_207015.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.814
Genes affected
NAALADL2 (HGNC:23219): (N-acetylated alpha-linked acidic dipeptidase like 2) Predicted to enable metalloexopeptidase activity. Predicted to be involved in proteolysis. Predicted to act upstream of or within response to bacterium. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAALADL2 | ENST00000454872.6 | c.1090+32995G>T | intron_variant | Intron 5 of 13 | 1 | NM_207015.3 | ENSP00000404705.1 | |||
NAALADL2 | ENST00000414826.1 | n.121-89909G>T | intron_variant | Intron 1 of 6 | 1 | ENSP00000396969.1 | ||||
NAALADL2 | ENST00000473253.5 | n.1322+32995G>T | intron_variant | Intron 5 of 10 | 2 | |||||
NAALADL2 | ENST00000489299.5 | n.829+32995G>T | intron_variant | Intron 5 of 10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.282 AC: 42858AN: 151816Hom.: 6349 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.282 AC: 42873AN: 151934Hom.: 6348 Cov.: 32 AF XY: 0.287 AC XY: 21300AN XY: 74232
GnomAD4 genome
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42873
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32
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21300
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Asia WGS
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1265
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3474
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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