rs9858278

Variant names:

• chr3-175736887-T-C
• rs9858278
• NM_207015.3:c.1897-419T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-175736887-T-C
• chr3-175736887-T-G

Variant summary

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

The NM_207015.3(NAALADL2):​c.1897-419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,036 control chromosomes in the GnomAD database, including 15,888 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 0.41 (15888 hom., cov: 33)
• Consequence: NAALADL2 NM_207015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAALADL2	NM_207015.3	c.1897-419T>C		intron_variant	Intron 11 of 13	ENST00000454872.6	NP_996898.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAALADL2	ENST00000454872.6	c.1897-419T>C		intron_variant	Intron 11 of 13	1	NM_207015.3	ENSP00000404705.1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62059 AN: 151918 Hom.: 15854 Cov.: 33

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0910

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.409 AC: 62149 AN: 152036 Hom.: 15888 Cov.: 33 AF XY: 0.402 AC XY: 29894 AN XY: 74334

African (AFR) AF: 0.728 AC: 30184 AN: 41472

American (AMR) AF: 0.342 AC: 5221 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3470

East Asian (EAS) AF: 0.0913 AC: 472 AN: 5172

South Asian (SAS) AF: 0.272 AC: 1316 AN: 4830

European-Finnish (FIN) AF: 0.248 AC: 2615 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20015 AN: 67926

Other (OTH) AF: 0.392 AC: 827 AN: 2112

Alfa AF: 0.295 Hom.: 3664

Bravo AF: 0.429

Asia WGS AF: 0.244 AC: 849 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.031
DANN	Benign	0.70
PhyloP100		-2.0
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: rs9858278; hg19: chr3-175454675;