rs17696736

chr12-112049014-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAA25	NM_024953.4	c.1729-571T>C		intron_variant		ENST00000261745.9
LOC124903022	XR_007063465.1	n.1959+2403A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA25	ENST00000261745.9	c.1729-571T>C		intron_variant		1	NM_024953.4	P1
NAA25	ENST00000549711.5	c.*1435+469T>C		intron_variant, NMD_transcript_variant		1
NAA25	ENST00000551858.1	c.*1816-571T>C		intron_variant, NMD_transcript_variant		1
NAA25	ENST00000552527.5	n.1741-571T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0724

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.322

Alfa AF: 0.411 Hom.: 32409

Bravo AF: 0.281

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	16
DANN	Benign	0.55

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: rs17696736; hg19: chr12-112486818;