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GeneBe

rs17696736

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0850
Variant links:
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]

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ACMG classification

Classification made for transcript

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
NAA25NM_024953.4 linkuse as main transcriptc.1729-571T>C intron_variant ENST00000261745.9
LOC124903022XR_007063465.1 linkuse as main transcriptn.1959+2403A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAA25ENST00000261745.9 linkuse as main transcriptc.1729-571T>C intron_variant 1 NM_024953.4 P1Q14CX7-1
NAA25ENST00000549711.5 linkuse as main transcriptc.*1435+469T>C intron_variant, NMD_transcript_variant 1
NAA25ENST00000551858.1 linkuse as main transcriptc.*1816-571T>C intron_variant, NMD_transcript_variant 1
NAA25ENST00000552527.5 linkuse as main transcriptn.1741-571T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.295
AC:
44893
AN:
151964
Hom.:
9165
Cov.:
32
show subpopulations
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
show subpopulations
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17696736; hg19: chr12-112486818; API