rs13319550

Variant names:

• chr3-175057780-A-G
• rs13319550
• NM_207015.3:c.44-39010A>G

Variant summary

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

The NM_207015.3(NAALADL2):​c.44-39010A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0487 in 152,318 control chromosomes in the GnomAD database, including 208 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 0.049 (208 hom., cov: 32)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 3 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]

LOC124906305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0616 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207015.3. 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
	NAALADL2	NM_207015.3	MANE Select	c.44-39010A>G		intron	N/A	NP_996898.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAALADL2	ENST00000454872.6	TSL:1 MANE Select	c.44-39010A>G		intron	N/A	ENSP00000404705.1
	NAALADL2	ENST00000485853.5	TSL:1	n.130-39010A>G		intron	N/A
	NAALADL2	ENST00000434257.1	TSL:4	c.-8-39010A>G		intron	N/A	ENSP00000409858.1

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7417 AN: 152200 Hom.: 209 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0366

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0487 AC: 7415 AN: 152318 Hom.: 208 Cov.: 32 AF XY: 0.0460 AC XY: 3427 AN XY: 74476

African (AFR) AF: 0.0306 AC: 1271 AN: 41572

American (AMR) AF: 0.0442 AC: 676 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.00559 AC: 29 AN: 5184

South Asian (SAS) AF: 0.0296 AC: 143 AN: 4828

European-Finnish (FIN) AF: 0.0366 AC: 389 AN: 10620

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0631 AC: 4296 AN: 68032

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0524 Hom.: 113

Bravo AF: 0.0489

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	7.1
DANN	Benign	0.53
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs13319550; hg19: chr3-174775570;