rs11066132

Variant names:

• chr12-112030402-C-T
• rs11066132
• NM_024953.4:c.2797-749G>A

Variant summary

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

The NM_024953.4(NAA25):​c.2797-749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00789 in 152,084 control chromosomes in the GnomAD database, including 140 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 0.0079 (140 hom., cov: 31)
• Consequence: NAA25 NM_024953.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 10 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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAA25	NM_024953.4	c.2797-749G>A		intron_variant	Intron 23 of 23	ENST00000261745.9	NP_079229.2
NAA25	XM_006719606.3	c.2713-749G>A		intron_variant	Intron 23 of 23		XP_006719669.1
NAA25	XM_047429557.1	c.2389-749G>A		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.2797-749G>A		intron_variant	Intron 23 of 23	1	NM_024953.4	ENSP00000261745.4
NAA25	ENST00000549711.5	n.*2504-749G>A		intron_variant	Intron 23 of 23	1		ENSP00000448200.1
NAA25	ENST00000548181.1	n.2174-749G>A		intron_variant	Intron 1 of 1	2
NAA25	ENST00000552527.5	n.3950-749G>A		intron_variant	Intron 22 of 22	2

Frequencies

GnomAD3 genomes AF: 0.00792 AC: 1203 AN: 151966 Hom.: 140 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000853

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.0000948

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00527

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

GnomAD4 genome AF: 0.00789 AC: 1200 AN: 152084 Hom.: 140 Cov.: 31 AF XY: 0.00920 AC XY: 684 AN XY: 74348

African (AFR) AF: 0.00 AC: 0 AN: 41500

American (AMR) AF: 0.000852 AC: 13 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1170 AN: 5166

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4824

European-Finnish (FIN) AF: 0.0000948 AC: 1 AN: 10548

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68000

Other (OTH) AF: 0.00474 AC: 10 AN: 2110

Alfa AF: 0.00205 Hom.: 1

Bravo AF: 0.00890

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	2.0
DANN	Benign	0.77
PhyloP100		-0.24
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: rs11066132; hg19: chr12-112468206;