rs13319550

chr3-175057780-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAALADL2	NM_207015.3	c.44-39010A>G		intron_variant		ENST00000454872.6
LOC124906305	XR_007096173.1	n.152+733T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAALADL2	ENST00000454872.6	c.44-39010A>G		intron_variant		1	NM_207015.3	P1
NAALADL2	ENST00000485853.5	n.130-39010A>G		intron_variant, non_coding_transcript_variant		1
NAALADL2	ENST00000434257.1	c.-8-39010A>G		intron_variant		4
NAALADL2	ENST00000473253.5	n.276-39010A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.0442

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.0366

Gnomad4 NFE AF: 0.0631

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0574 Hom.: 66

Bravo AF: 0.0489

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	7.1
Dann	Benign	0.53

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: rs13319550; hg19: chr3-174775570;