3-174863036-T-G

Variant names:

• chr3-174863036-T-G
• rs2222447
• NM_207015.3:c.43+3586T>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.43+3586T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,926 control chromosomes in the GnomAD database, including 38,784 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 0.71 (38784 hom., cov: 32)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAALADL2	NM_207015.3	c.43+3586T>G		intron_variant	Intron 1 of 13	ENST00000454872.6	NP_996898.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAALADL2	ENST00000454872.6	c.43+3586T>G		intron_variant	Intron 1 of 13	1	NM_207015.3	ENSP00000404705.1
NAALADL2	ENST00000485853.5	n.129+3586T>G		intron_variant	Intron 1 of 3	1
NAALADL2	ENST00000434257.1	c.-9+125290T>G		intron_variant	Intron 3 of 3	4		ENSP00000409858.1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107274 AN: 151808 Hom.: 38744 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.707 AC: 107376 AN: 151926 Hom.: 38784 Cov.: 32 AF XY: 0.710 AC XY: 52727 AN XY: 74250

African (AFR) AF: 0.861 AC: 35694 AN: 41464

American (AMR) AF: 0.661 AC: 10060 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2095 AN: 3470

East Asian (EAS) AF: 0.805 AC: 4148 AN: 5150

South Asian (SAS) AF: 0.681 AC: 3283 AN: 4820

European-Finnish (FIN) AF: 0.722 AC: 7631 AN: 10568

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42152 AN: 67914

Other (OTH) AF: 0.679 AC: 1432 AN: 2108

Alfa AF: 0.650 Hom.: 18651

Bravo AF: 0.708

Asia WGS AF: 0.737 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.54
PhyloP100		-0.45
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

Publications

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Other links and lift over

dbSNP: rs2222447; hg19: chr3-174580826;