rs6806492

Variant names:

• chr3-174992910-G-A
• rs6806492
• NM_207015.3:c.44-103880G>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.44-103880G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,956 control chromosomes in the GnomAD database, including 6,070 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 0.26 (6070 hom., cov: 32)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAALADL2	NM_207015.3	MANE Select	c.44-103880G>A		intron	N/A	NP_996898.2	Q58DX5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAALADL2	ENST00000454872.6	TSL:1 MANE Select	c.44-103880G>A		intron	N/A	ENSP00000404705.1	Q58DX5-1
	NAALADL2	ENST00000485853.5	TSL:1	n.130-103880G>A		intron	N/A
	NAALADL2	ENST00000434257.1	TSL:4	c.-8-103880G>A		intron	N/A	ENSP00000409858.1	C9JQ86

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39086 AN: 151838 Hom.: 6060 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.258 AC: 39133 AN: 151956 Hom.: 6070 Cov.: 32 AF XY: 0.257 AC XY: 19097 AN XY: 74278

African (AFR) AF: 0.425 AC: 17619 AN: 41430

American (AMR) AF: 0.239 AC: 3638 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.402 AC: 2069 AN: 5148

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10600

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11647 AN: 67940

Other (OTH) AF: 0.281 AC: 591 AN: 2106

Alfa AF: 0.203 Hom.: 12266

Bravo AF: 0.277

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.22
PhyloP100		-0.19
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: rs6806492; hg19: chr3-174710700;