rs7432623

chr3-175021543-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.44-75247G>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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAALADL2	NM_207015.3	c.44-75247G>A		intron_variant		ENST00000454872.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAALADL2	ENST00000454872.6	c.44-75247G>A		intron_variant		1	NM_207015.3	P1
NAALADL2	ENST00000485853.5	n.130-75247G>A		intron_variant, non_coding_transcript_variant		1
NAALADL2	ENST00000434257.1	c.-8-75247G>A		intron_variant		4
NAALADL2	ENST00000473253.5	n.276-75247G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0966

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.293

Alfa AF: 0.197 Hom.: 1811

Bravo AF: 0.314

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.0070
Dann	Benign	0.48

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: rs7432623; hg19: chr3-174739333;