ENST00000489729.5:n.179-52845C>T

Variant names:

• chr3-174684796-C-T
• rs12493995
• ENST00000489729.5:n.179-52845C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000489729.5(NAALADL2):​n.179-52845C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0796 in 151,966 control chromosomes in the GnomAD database, including 697 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 0.080 (697 hom., cov: 31)
• Consequence: NAALADL2 ENST00000489729.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000489729.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAALADL2	ENST00000489729.5	TSL:1	n.179-52845C>T		intron	N/A
	NAALADL2	ENST00000491329.5	TSL:1	n.171-7177C>T		intron	N/A
	NAALADL2	ENST00000434257.1	TSL:4	c.-114-52845C>T		intron	N/A	ENSP00000409858.1

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12101 AN: 151846 Hom.: 700 Cov.: 31

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0795

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0796 AC: 12096 AN: 151966 Hom.: 697 Cov.: 31 AF XY: 0.0846 AC XY: 6283 AN XY: 74278

African (AFR) AF: 0.0823 AC: 3409 AN: 41440

American (AMR) AF: 0.0917 AC: 1398 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1275 AN: 5162

South Asian (SAS) AF: 0.274 AC: 1319 AN: 4814

European-Finnish (FIN) AF: 0.0534 AC: 564 AN: 10570

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3756 AN: 67956

Other (OTH) AF: 0.0782 AC: 165 AN: 2110

Alfa AF: 0.0716 Hom.: 347

Bravo AF: 0.0789

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.74
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs12493995; hg19: chr3-174402586;