dbSNP rs144163075: NAA38:p.Trp56* (chr17-7857256-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_032356.6(NAA38):c.168G>A(p.Trp56*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,610,054 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0090 ( 15 hom., cov: 32)

Exomes 𝑓: 0.013 ( 142 hom. )

Consequence

NAA38
NM_032356.6 stop_gained

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.51

Publications

6 publications found

Variant links:

Genes affected

NAA38 (HGNC:28212): (N-alpha-acetyltransferase 38, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex. Colocalizes with polysome. [provided by Alliance of Genome Resources, Apr 2022]

NAA38 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP6

Variant 17-7857256-C-T is Benign according to our data. Variant chr17-7857256-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 808218.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 1366 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032356.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NAA38	NM_001320925.4	MANE Select	c.82-58G>A		intron	N/A	NP_001307854.1	Q9BRA0-1
NAA38	NM_032356.6		c.168G>A	p.Trp56*	stop_gained	Exon 1 of 2	NP_115732.2
NAA38	NM_001320924.3		c.82-58G>A		intron	N/A	NP_001307853.1	I3L3Z2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NAA38	ENST00000333775.9	TSL:1	c.168G>A	p.Trp56*	stop_gained	Exon 1 of 2	ENSP00000332103.5	Q9BRA0-2
NAA38	ENST00000575771.6	TSL:1 MANE Select	c.82-58G>A		intron	N/A	ENSP00000460172.2	Q9BRA0-1
NAA38	ENST00000576384.1	TSL:2	c.-133G>A		5_prime_UTR	Exon 1 of 2	ENSP00000460085.1	I3L310

Frequencies

GnomAD3 genomes

AF:

0.00898

AC:

1366

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00282

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.00824

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.00273

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0143

Gnomad OTH

AF:

0.00860

GnomAD2 exomes

AF:

0.00926

AC:

2227

AN:

240582

AF XY:

0.00967

show subpopulations

Gnomad AFR exome

AF:

0.00287

Gnomad AMR exome

AF:

0.00644

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00224

Gnomad NFE exome

AF:

0.0153

Gnomad OTH exome

AF:

0.0114

GnomAD4 exome

AF:

0.0125

AC:

18268

AN:

1457804

Hom.:

142

Cov.:

AF XY:

0.0124

AC XY:

8982

AN XY:

724646

show subpopulations

African (AFR)

AF:

0.00248

AC:

AN:

33406

American (AMR)

AF:

0.00691

AC:

308

AN:

44582

Ashkenazi Jewish (ASJ)

AF:

0.0147

AC:

384

AN:

26058

East Asian (EAS)

AF:

0.0000253

AC:

AN:

39604

South Asian (SAS)

AF:

0.00297

AC:

256

AN:

86130

European-Finnish (FIN)

AF:

0.00299

AC:

156

AN:

52102

Middle Eastern (MID)

AF:

0.0157

AC:

AN:

5724

European-Non Finnish (NFE)

AF:

0.0147

AC:

16358

AN:

1109986

Other (OTH)

AF:

0.0105

AC:

632

AN:

60212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

1114

2227

3341

4454

5568

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

600

1200

1800

2400

3000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00897

AC:

1366

AN:

152250

Hom.:

Cov.:

AF XY:

0.00830

AC XY:

618

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.00281

AC:

117

AN:

41584

American (AMR)

AF:

0.00823

AC:

126

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.0133

AC:

AN:

3470

East Asian (EAS)

AF:

0.000196

AC:

AN:

5106

South Asian (SAS)

AF:

0.00331

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00273

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0143

AC:

974

AN:

68004

Other (OTH)

AF:

0.00851

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

132

198

264

330

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00971

Hom.:

Bravo

AF:

0.00921

TwinsUK

AF:

0.00782

AC:

ALSPAC

AF:

0.0104

AC:

ESP6500AA

AF:

0.00185

AC:

ESP6500EA

AF:

0.0135

AC:

114

ExAC

AF:

0.00895

AC:

1078

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0178

EpiControl

AF:

0.0202

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.25

BayesDel_noAF

Pathogenic

0.60

CADD

Benign

(source)

DANN

Uncertain

0.99

Eigen

Pathogenic

1.0

Eigen_PC

Pathogenic

0.86

FATHMM_MKL

Uncertain

0.89

PhyloP100

2.5

Vest4

0.12

GERP RS

5.3

PromoterAI

-0.024

Neutral

(source)

Mutation Taster

=159/41

disease causing (fs/PTC)

(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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over