chr12-112049014-A-G

Variant names:

• chr12-112049014-A-G
• rs17696736
• NM_024953.4:c.1729-571T>C

Variant summary

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

The NM_024953.4(NAA25):​c.1729-571T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,082 control chromosomes in the GnomAD database, including 9,161 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 0.30 (9161 hom., cov: 32)
• Consequence: NAA25 NM_024953.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 164 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]

LOC124903022 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 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.1729-571T>C		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.1729-571T>C		intron	N/A	ENSP00000261745.4
	NAA25	ENST00000549711.5	TSL:1	n.*1435+469T>C		intron	N/A	ENSP00000448200.1
	NAA25	ENST00000551858.1	TSL:1	n.*1816-571T>C		intron	N/A	ENSP00000446719.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44893 AN: 151964 Hom.: 9165 Cov.: 32

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.295 AC: 44874 AN: 152082 Hom.: 9161 Cov.: 32 AF XY: 0.287 AC XY: 21305 AN XY: 74320

African (AFR) AF: 0.0724 AC: 3008 AN: 41528

American (AMR) AF: 0.264 AC: 4034 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2268 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.0826 AC: 399 AN: 4830

European-Finnish (FIN) AF: 0.401 AC: 4227 AN: 10534

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29774 AN: 67954

Other (OTH) AF: 0.322 AC: 682 AN: 2116

Alfa AF: 0.394 Hom.: 59687

Bravo AF: 0.281

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	16
DANN	Benign	0.55
PhyloP100		0.085
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: rs17696736; hg19: chr12-112486818;