NM_024953.4:c.403-2510C>T

Variant names:

• chr12-112083644-G-A
• rs4767364
• NM_024953.4:c.403-2510C>T

Variant summary

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

The NM_024953.4(NAA25):​c.403-2510C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,102 control chromosomes in the GnomAD database, including 20,093 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 0.46 (20093 hom., cov: 32)
• Consequence: NAA25 NM_024953.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 60 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024953.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA25	NM_024953.4	MANE Select	c.403-2510C>T		intron	N/A	NP_079229.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA25	ENST00000261745.9	TSL:1 MANE Select	c.403-2510C>T		intron	N/A	ENSP00000261745.4
	NAA25	ENST00000549711.5	TSL:1	n.284-2510C>T		intron	N/A	ENSP00000448200.1
	NAA25	ENST00000551858.1	TSL:1	n.*490-2510C>T		intron	N/A	ENSP00000446719.1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69289 AN: 151984 Hom.: 20038 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.456 AC: 69407 AN: 152102 Hom.: 20093 Cov.: 32 AF XY: 0.460 AC XY: 34233 AN XY: 74356

African (AFR) AF: 0.773 AC: 32079 AN: 41496

American (AMR) AF: 0.435 AC: 6642 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3472

East Asian (EAS) AF: 0.903 AC: 4682 AN: 5184

South Asian (SAS) AF: 0.587 AC: 2833 AN: 4824

European-Finnish (FIN) AF: 0.233 AC: 2460 AN: 10576

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18905 AN: 67958

Other (OTH) AF: 0.430 AC: 906 AN: 2108

Alfa AF: 0.334 Hom.: 37821

Bravo AF: 0.485

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-1.5
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: rs4767364; hg19: chr12-112521448;