3-175354813-C-T

Variant names:

• chr3-175354813-C-T
• rs9809218
• NM_207015.3:c.1090+30488C>T

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+30488C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 150,960 control chromosomes in the GnomAD database, including 1,227 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 0.074 (1227 hom., cov: 31)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAALADL2	NM_207015.3	c.1090+30488C>T		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+30488C>T		intron_variant	Intron 5 of 13	1	NM_207015.3	ENSP00000404705.1
NAALADL2	ENST00000414826.1	n.121-92416C>T		intron_variant	Intron 1 of 6	1		ENSP00000396969.1
NAALADL2	ENST00000473253.5	n.1322+30488C>T		intron_variant	Intron 5 of 10	2
NAALADL2	ENST00000489299.5	n.829+30488C>T		intron_variant	Intron 5 of 10	2

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11131 AN: 150850 Hom.: 1220 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0348

Gnomad ASJ AF: 0.0145

Gnomad EAS AF: 0.00294

Gnomad SAS AF: 0.00440

Gnomad FIN AF: 0.00135

Gnomad MID AF: 0.0162

Gnomad NFE AF: 0.00559

Gnomad OTH AF: 0.0514

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

GnomAD4 genome AF: 0.0740 AC: 11167 AN: 150960 Hom.: 1227 Cov.: 31 AF XY: 0.0715 AC XY: 5271 AN XY: 73752

African (AFR) AF: 0.245 AC: 10051 AN: 41030

American (AMR) AF: 0.0347 AC: 526 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.0145 AC: 50 AN: 3454

East Asian (EAS) AF: 0.00275 AC: 14 AN: 5086

South Asian (SAS) AF: 0.00441 AC: 21 AN: 4766

European-Finnish (FIN) AF: 0.00135 AC: 14 AN: 10392

Middle Eastern (MID) AF: 0.0175 AC: 5 AN: 286

European-Non Finnish (NFE) AF: 0.00559 AC: 379 AN: 67776

Other (OTH) AF: 0.0509 AC: 107 AN: 2104

Alfa AF: 0.0709 Hom.: 709

Bravo AF: 0.0847

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	10
DANN	Benign	0.46
PhyloP100		0.28
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: rs9809218; hg19: chr3-175072602;