chr3-175385825-G-T

Variant names:

• chr3-175385825-G-T
• rs62287976
• NM_207015.3:c.1091-61404G>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.1091-61404G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,776 control chromosomes in the GnomAD database, including 9,882 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 0.34 (9882 hom., cov: 31)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAALADL2	NM_207015.3	c.1091-61404G>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.1091-61404G>T		intron_variant	Intron 5 of 13	1	NM_207015.3	ENSP00000404705.1
NAALADL2	ENST00000414826.1	n.121-61404G>T		intron_variant	Intron 1 of 6	1		ENSP00000396969.1
NAALADL2	ENST00000473253.5	n.1323-61404G>T		intron_variant	Intron 5 of 10	2
NAALADL2	ENST00000489299.5	n.829+61500G>T		intron_variant	Intron 5 of 10	2

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52103 AN: 151658 Hom.: 9862 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.344 AC: 52163 AN: 151776 Hom.: 9882 Cov.: 31 AF XY: 0.352 AC XY: 26106 AN XY: 74128

African (AFR) AF: 0.204 AC: 8471 AN: 41428

American (AMR) AF: 0.435 AC: 6627 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3119 AN: 5146

South Asian (SAS) AF: 0.377 AC: 1805 AN: 4792

European-Finnish (FIN) AF: 0.495 AC: 5201 AN: 10516

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24824 AN: 67886

Other (OTH) AF: 0.333 AC: 701 AN: 2108

Alfa AF: 0.315 Hom.: 3076

Bravo AF: 0.337

Asia WGS AF: 0.480 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.18
PhyloP100		-0.84
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: rs62287976; hg19: chr3-175103614;