Variant 12-112033286-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000261745.9(NAA25):c.2743C>A(p.Leu915Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0825 in 1,612,044 control chromosomes in the GnomAD database, including 7,437 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.13 ( 1944 hom., cov: 32)

Exomes 𝑓: 0.078 ( 5493 hom. )

Consequence

NAA25
ENST00000261745.9 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.12

Variant links:

Genes affected

NAA25 (HGNC:25783): (N-alpha-acetyltransferase 25, NatB auxiliary subunit) This gene encodes the auxiliary subunit of the heteromeric N-terminal acetyltransferase B complex. This complex acetylates methionine residues that are followed by acidic or asparagine residues.[provided by RefSeq, Mar 2010]

NAA25 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001417309).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
NAA25	NM_024953.4 linkuse as main transcript	c.2743C>A	p.Leu915Ile	missense_variant	23/24	ENST00000261745.9	NP_079229.2
NAA25	XM_006719606.3 linkuse as main transcript	c.2659C>A	p.Leu887Ile	missense_variant	23/24		XP_006719669.1
NAA25	XM_047429557.1 linkuse as main transcript	c.2335C>A	p.Leu779Ile	missense_variant	20/21		XP_047285513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAA25	ENST00000261745.9 linkuse as main transcript	c.2743C>A	p.Leu915Ile	missense_variant	23/24	1	NM_024953.4	ENSP00000261745	P1	Q14CX7-1
NAA25	ENST00000549711.5 linkuse as main transcript	c.*2450C>A		3_prime_UTR_variant, NMD_transcript_variant	23/24	1		ENSP00000448200
NAA25	ENST00000548181.1 linkuse as main transcript	n.2120C>A		non_coding_transcript_exon_variant	1/2	2
NAA25	ENST00000552527.5 linkuse as main transcript	n.3896C>A		non_coding_transcript_exon_variant	22/23	2

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19585

AN:

152068

Hom.:

1929

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.0950

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.000576

Gnomad SAS

AF:

0.0408

Gnomad FIN

AF:

0.0403

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0785

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.0759

AC:

18991

AN:

250334

Hom.:

1218

AF XY:

0.0719

AC XY:

9738

AN XY:

135352

show subpopulations

Gnomad AFR exome

AF:

0.279

Gnomad AMR exome

AF:

0.0643

Gnomad ASJ exome

AF:

0.0637

Gnomad EAS exome

AF:

0.000164

Gnomad SAS exome

AF:

0.0413

Gnomad FIN exome

AF:

0.0337

Gnomad NFE exome

AF:

0.0808

Gnomad OTH exome

AF:

0.0768

GnomAD4 exome

AF:

0.0777

AC:

113412

AN:

1459858

Hom.:

5493

Cov.:

AF XY:

0.0756

AC XY:

54933

AN XY:

726284

show subpopulations

Gnomad4 AFR exome

AF:

0.283

Gnomad4 AMR exome

AF:

0.0671

Gnomad4 ASJ exome

AF:

0.0646

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.0409

Gnomad4 FIN exome

AF:

0.0354

Gnomad4 NFE exome

AF:

0.0793

Gnomad4 OTH exome

AF:

0.0829

GnomAD4 genome

AF:

0.129

AC:

19635

AN:

152186

Hom.:

1944

Cov.:

AF XY:

0.124

AC XY:

9204

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.279

Gnomad4 AMR

AF:

0.0948

Gnomad4 ASJ

AF:

0.0608

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0410

Gnomad4 FIN

AF:

0.0403

Gnomad4 NFE

AF:

0.0785

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.0834

Hom.:

1498

Bravo

AF:

0.141

TwinsUK

AF:

0.0763

AC:

283

ALSPAC

AF:

0.0848

AC:

327

ESP6500AA

AF:

0.257

AC:

1133

ESP6500EA

AF:

0.0731

AC:

629

ExAC

AF:

0.0811

AC:

9841

Asia WGS

AF:

0.0330

AC:

117

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.018

Eigen

Uncertain

0.36

Eigen_PC

Uncertain

0.46

FATHMM_MKL

Uncertain

0.91

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0014

MetaSVM

Benign

-0.98

MutationAssessor

Benign

2.0

MutationTaster

Benign

0.023

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-0.62

REVEL

Benign

0.083

Sift

Benign

0.12

Sift4G

Benign

0.21

Polyphen

0.96

Vest4

0.048

MPC

0.064

ClinPred

0.018

GERP RS

5.0

Varity_R

0.16

gMVP

0.089

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

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