rs9878945

Positions:

• chr3-175022599-G-A

Variant summary

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

The NM_207015.3(NAALADL2):​c.44-74191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,950 control chromosomes in the GnomAD database, including 2,409 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 0.16 (2409 hom., cov: 32)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

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=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAALADL2	NM_207015.3	c.44-74191G>A		intron_variant		ENST00000454872.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAALADL2	ENST00000454872.6	c.44-74191G>A		intron_variant		1	NM_207015.3	P1
NAALADL2	ENST00000485853.5	n.130-74191G>A		intron_variant, non_coding_transcript_variant		1
NAALADL2	ENST00000434257.1	c.-8-74191G>A		intron_variant		4
NAALADL2	ENST00000473253.5	n.276-74191G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23927 AN: 151830 Hom.: 2403 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.158 AC: 23983 AN: 151950 Hom.: 2409 Cov.: 32 AF XY: 0.160 AC XY: 11852 AN XY: 74252

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.161

Alfa AF: 0.107 Hom.: 1823

Bravo AF: 0.176

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.46

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: rs9878945; hg19: chr3-174740389;