rs10507236

chr12-112030635-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024953.4(NAA25):c.2797-982A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,258 control chromosomes in the GnomAD database, including 1,310 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 0.056 (1310 hom., cov: 32)
• Consequence: NAA25 NM_024953.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAA25	NM_024953.4	c.2797-982A>G		intron_variant		ENST00000261745.9
NAA25	XM_006719606.3	c.2713-982A>G		intron_variant
NAA25	XM_047429557.1	c.2389-982A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA25	ENST00000261745.9	c.2797-982A>G		intron_variant		1	NM_024953.4	P1
NAA25	ENST00000549711.5	c.*2504-982A>G		intron_variant, NMD_transcript_variant		1
NAA25	ENST00000548181.1	n.2174-982A>G		intron_variant, non_coding_transcript_variant		2
NAA25	ENST00000552527.5	n.3950-982A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8450 AN: 152140 Hom.: 1315 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00315

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0555 AC: 8455 AN: 152258 Hom.: 1310 Cov.: 32 AF XY: 0.0620 AC XY: 4620 AN XY: 74458

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.00207

Gnomad4 NFE AF: 0.00315

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0294 Hom.: 246

Bravo AF: 0.0707

Asia WGS AF: 0.246 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.5
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10507236; hg19: chr12-112468439;