12-112083644-G-A

Position:

• chr12-112083644-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAA25	NM_024953.4	c.403-2510C>T		intron_variant		ENST00000261745.9	NP_079229.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAA25	ENST00000261745.9	c.403-2510C>T		intron_variant		1	NM_024953.4	ENSP00000261745	P1

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

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.430

Alfa AF: 0.320 Hom.: 14931

Bravo AF: 0.485

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs4767364; hg19: chr12-112521448;