NM_207015.3:c.44-75247G>A

Variant names:

• chr3-175021543-G-A
• rs7432623
• NM_207015.3:c.44-75247G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207015.3(NAALADL2):​c.44-75247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,820 control chromosomes in the GnomAD database, including 9,475 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 0.29 (9475 hom., cov: 32)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207015.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAALADL2	NM_207015.3	MANE Select	c.44-75247G>A		intron	N/A	NP_996898.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAALADL2	ENST00000454872.6	TSL:1 MANE Select	c.44-75247G>A		intron	N/A	ENSP00000404705.1
	NAALADL2	ENST00000485853.5	TSL:1	n.130-75247G>A		intron	N/A
	NAALADL2	ENST00000434257.1	TSL:4	c.-8-75247G>A		intron	N/A	ENSP00000409858.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43878 AN: 151700 Hom.: 9444 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.290 AC: 43963 AN: 151820 Hom.: 9475 Cov.: 32 AF XY: 0.282 AC XY: 20943 AN XY: 74208

African (AFR) AF: 0.613 AC: 25352 AN: 41384

American (AMR) AF: 0.196 AC: 2989 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 789 AN: 3464

East Asian (EAS) AF: 0.0966 AC: 497 AN: 5144

South Asian (SAS) AF: 0.138 AC: 663 AN: 4816

European-Finnish (FIN) AF: 0.103 AC: 1095 AN: 10584

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11720 AN: 67894

Other (OTH) AF: 0.293 AC: 617 AN: 2104

Alfa AF: 0.202 Hom.: 2148

Bravo AF: 0.314

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0070
DANN	Benign	0.48
PhyloP100		-1.5
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: rs7432623; hg19: chr3-174739333;