rs10507236

Variant names:

• chr12-112030635-T-C
• rs10507236
• NM_024953.4:c.2797-982A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NAA25	NM_024953.4	c.2797-982A>G		intron_variant	Intron 23 of 23	ENST00000261745.9	NP_079229.2
NAA25	XM_006719606.3	c.2713-982A>G		intron_variant	Intron 23 of 23		XP_006719669.1
NAA25	XM_047429557.1	c.2389-982A>G		intron_variant	Intron 20 of 20		XP_047285513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAA25	ENST00000261745.9	c.2797-982A>G		intron_variant	Intron 23 of 23	1	NM_024953.4	ENSP00000261745.4
NAA25	ENST00000549711.5	n.*2504-982A>G		intron_variant	Intron 23 of 23	1		ENSP00000448200.1
NAA25	ENST00000548181.1	n.2174-982A>G		intron_variant	Intron 1 of 1	2
NAA25	ENST00000552527.5	n.3950-982A>G		intron_variant	Intron 22 of 22	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

African (AFR) AF: 0.0532 AC: 2213 AN: 41564

American (AMR) AF: 0.144 AC: 2198 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3171 AN: 5168

South Asian (SAS) AF: 0.0977 AC: 471 AN: 4822

European-Finnish (FIN) AF: 0.00207 AC: 22 AN: 10622

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00315 AC: 214 AN: 68026

Other (OTH) AF: 0.0626 AC: 132 AN: 2108

Alfa AF: 0.0328 Hom.: 348

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
PhyloP100		0.84
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10507236; hg19: chr12-112468439;