rs3914502

Variant names:

• chr3-174846812-T-A
• rs3914502
• ENST00000434257.1:c.-9+109066T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-174846812-T-A
• chr3-174846812-T-C
• chr3-174846812-T-G

Variant summary

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

The ENST00000434257.1(NAALADL2):​c.-9+109066T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,958 control chromosomes in the GnomAD database, including 38,822 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 0.71 (38822 hom., cov: 30)
• Consequence: NAALADL2 ENST00000434257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 4 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434257.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAALADL2	ENST00000434257.1	TSL:4	c.-9+109066T>A		intron	N/A	ENSP00000409858.1	C9JQ86

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107337 AN: 151840 Hom.: 38784 Cov.: 30

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.707 AC: 107437 AN: 151958 Hom.: 38822 Cov.: 30 AF XY: 0.711 AC XY: 52767 AN XY: 74238

African (AFR) AF: 0.861 AC: 35721 AN: 41480

American (AMR) AF: 0.660 AC: 10071 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4224 AN: 5150

South Asian (SAS) AF: 0.689 AC: 3315 AN: 4812

European-Finnish (FIN) AF: 0.724 AC: 7636 AN: 10542

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42057 AN: 67944

Other (OTH) AF: 0.682 AC: 1438 AN: 2108

Alfa AF: 0.521 Hom.: 1339

Bravo AF: 0.709

Asia WGS AF: 0.754 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.039
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3914502;

hg19: chr3-174564602;