3-175534948-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_207015.3(NAALADL2):c.1654-41093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00797 in 151,660 control chromosomes in the GnomAD database, including 4 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 0.0080 ( 4 hom., cov: 31)
Consequence
NAALADL2
NM_207015.3 intron
NM_207015.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.606
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAALADL2 | NM_207015.3 | c.1654-41093C>T | intron_variant | ENST00000454872.6 | NP_996898.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAALADL2 | ENST00000454872.6 | c.1654-41093C>T | intron_variant | 1 | NM_207015.3 | ENSP00000404705.1 | ||||
NAALADL2 | ENST00000473253.5 | n.1886-41093C>T | intron_variant | 2 | ||||||
NAALADL2 | ENST00000489299.5 | n.1249-41093C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00798 AC: 1209AN: 151566Hom.: 4 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00797 AC: 1209AN: 151660Hom.: 4 Cov.: 31 AF XY: 0.00733 AC XY: 543AN XY: 74108
GnomAD4 genome
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ClinVar
Not reported inComputational 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