rs13062041

chr3-175177154-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207015.3(NAALADL2):c.546-56777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,850 control chromosomes in the GnomAD database, including 14,095 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 0.42 (14095 hom., cov: 31)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAALADL2	NM_207015.3	c.546-56777C>T		intron_variant		ENST00000454872.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAALADL2	ENST00000454872.6	c.546-56777C>T		intron_variant		1	NM_207015.3	P1
NAALADL2	ENST00000485853.5	n.632-56777C>T		intron_variant, non_coding_transcript_variant		1
NAALADL2	ENST00000473253.5	n.778-56777C>T		intron_variant, non_coding_transcript_variant		2
NAALADL2	ENST00000489299.5	n.237-40922C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63845 AN: 151732 Hom.: 14085 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.421 AC: 63874 AN: 151850 Hom.: 14095 Cov.: 31 AF XY: 0.423 AC XY: 31420 AN XY: 74208

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.413

Alfa AF: 0.454 Hom.: 6850

Bravo AF: 0.414

Asia WGS AF: 0.415 AC: 1442 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs13062041; hg19: chr3-174894944;