3-175357320-G-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.814
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NAALADL2NM_207015.3 linkc.1090+32995G>T intron_variant Intron 5 of 13 ENST00000454872.6 NP_996898.2 Q58DX5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NAALADL2ENST00000454872.6 linkc.1090+32995G>T intron_variant Intron 5 of 13 1 NM_207015.3 ENSP00000404705.1 Q58DX5-1
NAALADL2ENST00000414826.1 linkn.121-89909G>T intron_variant Intron 1 of 6 1 ENSP00000396969.1 Q6H9J7
NAALADL2ENST00000473253.5 linkn.1322+32995G>T intron_variant Intron 5 of 10 2
NAALADL2ENST00000489299.5 linkn.829+32995G>T intron_variant Intron 5 of 10 2

Frequencies

GnomAD3 genomes
AF:
0.282
AC:
42858
AN:
151816
Hom.:
6349
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.223
Gnomad AMI
AF:
0.276
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.272
Gnomad EAS
AF:
0.495
Gnomad SAS
AF:
0.240
Gnomad FIN
AF:
0.381
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.282
Gnomad OTH
AF:
0.285
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.282
AC:
42873
AN:
151934
Hom.:
6348
Cov.:
32
AF XY:
0.287
AC XY:
21300
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.223
Gnomad4 AMR
AF:
0.320
Gnomad4 ASJ
AF:
0.272
Gnomad4 EAS
AF:
0.496
Gnomad4 SAS
AF:
0.238
Gnomad4 FIN
AF:
0.381
Gnomad4 NFE
AF:
0.282
Gnomad4 OTH
AF:
0.283
Alfa
AF:
0.272
Hom.:
11495
Bravo
AF:
0.280
Asia WGS
AF:
0.364
AC:
1265
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
9.4
DANN
Benign
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6771725; hg19: chr3-175075109; API