NM_207015.3:c.1090+13383C>G

Variant names:

• chr3-175337708-C-G
• rs6788338
• NM_207015.3:c.1090+13383C>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.1090+13383C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,936 control chromosomes in the GnomAD database, including 11,464 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 0.38 (11464 hom., cov: 32)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAALADL2	NM_207015.3	c.1090+13383C>G		intron_variant	Intron 5 of 13	ENST00000454872.6	NP_996898.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAALADL2	ENST00000454872.6	c.1090+13383C>G		intron_variant	Intron 5 of 13	1	NM_207015.3	ENSP00000404705.1
NAALADL2	ENST00000414826.1	n.120+81178C>G		intron_variant	Intron 1 of 6	1		ENSP00000396969.1
NAALADL2	ENST00000473253.5	n.1322+13383C>G		intron_variant	Intron 5 of 10	2
NAALADL2	ENST00000489299.5	n.829+13383C>G		intron_variant	Intron 5 of 10	2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58142 AN: 151816 Hom.: 11458 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.383 AC: 58176 AN: 151936 Hom.: 11464 Cov.: 32 AF XY: 0.382 AC XY: 28348 AN XY: 74254

African (AFR) AF: 0.306 AC: 12688 AN: 41448

American (AMR) AF: 0.331 AC: 5058 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1180 AN: 5164

South Asian (SAS) AF: 0.500 AC: 2412 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4661 AN: 10538

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29400 AN: 67926

Other (OTH) AF: 0.389 AC: 819 AN: 2106

Alfa AF: 0.409 Hom.: 1605

Bravo AF: 0.367

Asia WGS AF: 0.362 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.020
DANN	Benign	0.36
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs6788338; hg19: chr3-175055497;