rs17696736

Variant names:

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

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-4 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

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 cumulative frequency of 0.295 (AC=44,874) in the gnomAD database across 152,082 control chromosomes, including 9,161 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.434. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. 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: 166 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:):

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -4 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	B1High frequency in general population		GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.434 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

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

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	NAA25 NM_024953.4	MANE Select	c.1729-571T>C	intron	Intron 15 of 23	Prot: NP_079229.2

NAA25 NM_024953.4

MANE Select

HGVSc / HGVSpc.1729-571T>C

Exon rankIntron 15 of 23

intron

Prot: NP_079229.2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	NAA25 ENST00000261745.9	TSL:1MANE Select	c.1729-571T>C	intron	Intron 15 of 23	Prot: ENSP00000261745.4 UniProt:
	NAA25 ENST00000549711.5	TSL:1	n.*1435+469T>C	intron	Intron 15 of 23	Prot: ENSP00000448200.1 UniProt:
	NAA25 ENST00000551858.1	TSL:1	n.*1816-571T>C	intron	Intron 16 of 22	Prot: ENSP00000446719.1 UniProt:

NAA25 ENST00000261745.9

TSL:1MANE Select

HGVSc / HGVSpc.1729-571T>C

Exon rankIntron 15 of 23

intron

Prot: ENSP00000261745.4UniProt: Q14CX7-1

NAA25 ENST00000549711.5

TSL:1

HGVSc / HGVSpn.*1435+469T>C

Exon rankIntron 15 of 23

intron

Prot: ENSP00000448200.1UniProt: F8VSB9

NAA25 ENST00000551858.1

TSL:1

HGVSc / HGVSpn.*1816-571T>C

Exon rankIntron 16 of 22

intron

Prot: ENSP00000446719.1UniProt: F8W0N5

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.295	AC:44893	Hom:9165	AN:151964	Cov:32
GnomAD4 genome	AF: 0.295	AC:44874	Hom:9161	AN:152082	Cov:32
TOPMed (Bravo)	AF: 0.281	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.389	AC:292508	Hom:63747	AN:752032	Cov:
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.327	AC:765	Hom:142	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.00276	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.517	AC:155	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.0550	AC:191	Hom:	AN:3478	Cov:
Qatari Genome	AF: 0.171	AC:30	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.000383	AC:47	Hom:6	AN:122576	Cov:
Turkish Variome	AF: 0.390	AC:603	Hom:129	AN:1546	Cov:
UK10K	AF: 0.418	AC:3160	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.000558	AC:5	Hom:0	AN:8960	Cov:

Showing 13 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Uncertain	15
BayesDel_noAF	Benign	-0.78
CADD	Benign	16
DANN	Benign	0.55
GPN-Star LLR	N/A	-3.6
GPN-Star score	N/A	3.6
Mutation Taster	N/A	100/0	polymorphism (auto)
PhyloP100	Benign	0.085

Showing 8 of 8 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs17696736;

hg19: chr12-112486818;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar