dbSNP rs11732759: NAAA:c.*816A>T (chr4-75935287-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000507187.2(NAAA):c.*816A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,062 control chromosomes in the GnomAD database, including 9,999 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 0.34 ( 9999 hom., cov: 33)

Failed GnomAD Quality Control

Consequence

NAAA
ENST00000507187.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510

Publications

19 publications found

Variant links:

Genes affected

NAAA (HGNC:736): (N-acylethanolamine acid amidase) Enables N-(long-chain-acyl)ethanolamine deacylase activity; N-acylsphingosine amidohydrolase activity; and fatty acid amide hydrolase activity. Involved in several processes, including N-acylethanolamine metabolic process; N-acylphosphatidylethanolamine metabolic process; and sphingosine metabolic process. Located in lysosome. Is extrinsic component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

NAAA links:

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new If you want to explore the variant's impact on the transcript ENST00000507187.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507187.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NAAA	NM_014435.4	MANE Select	c.498+822A>T	intron	N/A	NP_055250.2	Q02083-1
NAAA	NM_001042402.2		c.498+822A>T	intron	N/A	NP_001035861.1	Q02083-2
NAAA	NM_001363719.2		c.498+822A>T	intron	N/A	NP_001350648.1	Q02083-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NAAA	ENST00000507187.2	TSL:1	c.*816A>T	3_prime_UTR	Exon 3 of 3	ENSP00000423142.1	D6R9S9
NAAA	ENST00000286733.9	TSL:5 MANE Select	c.498+822A>T	intron	N/A	ENSP00000286733.4	Q02083-1
NAAA	ENST00000967490.1		c.525+822A>T	intron	N/A	ENSP00000637549.1

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52194

AN:

151944

Hom.:

10005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.187

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.0680

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.483

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.333

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.343

AC:

52189

AN:

152062

Hom.:

9999

Cov.:

AF XY:

0.344

AC XY:

25587

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.243

AC:

10076

AN:

41504

American (AMR)

AF:

0.245

AC:

3738

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.402

AC:

1396

AN:

3470

East Asian (EAS)

AF:

0.0680

AC:

352

AN:

5180

South Asian (SAS)

AF:

0.431

AC:

2077

AN:

4820

European-Finnish (FIN)

AF:

0.483

AC:

5093

AN:

10540

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.419

AC:

28482

AN:

67958

Other (OTH)

AF:

0.332

AC:

702

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1712

3424

5136

6848

8560

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.383

Hom.:

1444

Bravo

AF:

0.314

Asia WGS

AF:

0.267

AC:

931

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

-0.051

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over