Variant chr3-174684796-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000489729.5(NAALADL2):n.179-52845C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0796 in 151,966 control chromosomes in the GnomAD database, including 697 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 0.080 ( 697 hom., cov: 31)

Consequence

NAALADL2
ENST00000489729.5 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.828

Variant links:

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]

NAALADL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
NAALADL2	XM_006713560.4 linkuse as main transcript	c.-114-52845C>T	intron_variant
NAALADL2	XM_017006071.2 linkuse as main transcript	c.-184-50090C>T	intron_variant
NAALADL2	XM_017006073.2 linkuse as main transcript	c.-198-7177C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
NAALADL2	ENST00000489729.5 linkuse as main transcript	n.179-52845C>T	intron_variant, non_coding_transcript_variant	1
NAALADL2	ENST00000491329.5 linkuse as main transcript	n.171-7177C>T	intron_variant, non_coding_transcript_variant	1
NAALADL2	ENST00000434257.1 linkuse as main transcript	c.-114-52845C>T	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.0797

AC:

12101

AN:

151846

Hom.:

700

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0823

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0917

Gnomad ASJ

AF:

0.0462

Gnomad EAS

AF:

0.246

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.0534

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0553

Gnomad OTH

AF:

0.0795

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

GnomAD4 genome

AF:

0.0796

AC:

12096

AN:

151966

Hom.:

697

Cov.:

AF XY:

0.0846

AC XY:

6283

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.0823

Gnomad4 AMR

AF:

0.0917

Gnomad4 ASJ

AF:

0.0462

Gnomad4 EAS

AF:

0.247

Gnomad4 SAS

AF:

0.274

Gnomad4 FIN

AF:

0.0534

Gnomad4 NFE

AF:

0.0553

Gnomad4 OTH

AF:

0.0782

Alfa

AF:

0.0728

Hom.:

327

Bravo

AF:

0.0789

Asia WGS

AF:

0.240

AC:

834

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.53

DANN

Benign

0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over