11-34113709-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024662.3(NAT10):​c.373-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00284 in 1,601,780 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 48 hom., cov: 31)
Exomes 𝑓: 0.0015 ( 46 hom. )

Consequence

NAT10
NM_024662.3 splice_region, intron

Scores

2
Splicing: ADA: 0.0001091
2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0370
Variant links:
Genes affected
NAT10 (HGNC:29830): (N-acetyltransferase 10) The protein encoded by this gene is an RNA cytidine acetyltransferase involved in histone acetylation, tRNA acetylation, the biosynthesis of 18S rRNA, and the enhancement of nuclear architecture and chromatin organization. [provided by RefSeq, Oct 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 11-34113709-C-T is Benign according to our data. Variant chr11-34113709-C-T is described in ClinVar as [Benign]. Clinvar id is 791313.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0513 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NAT10NM_024662.3 linkc.373-7C>T splice_region_variant, intron_variant Intron 4 of 28 ENST00000257829.8 NP_078938.3 Q9H0A0-1
NAT10NM_001144030.2 linkc.157-7C>T splice_region_variant, intron_variant Intron 2 of 26 NP_001137502.2 Q9H0A0-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NAT10ENST00000257829.8 linkc.373-7C>T splice_region_variant, intron_variant Intron 4 of 28 1 NM_024662.3 ENSP00000257829.3 Q9H0A0-1
NAT10ENST00000531159.6 linkc.157-7C>T splice_region_variant, intron_variant Intron 2 of 26 2 ENSP00000433011.2 Q9H0A0-2
NAT10ENST00000527971.5 linkc.373-7C>T splice_region_variant, intron_variant Intron 3 of 7 2 ENSP00000437324.1 E9PMU0
NAT10ENST00000529523.5 linkc.373-7C>T splice_region_variant, intron_variant Intron 4 of 4 4 ENSP00000435569.1 E9PJN6

Frequencies

GnomAD3 genomes
AF:
0.0151
AC:
2281
AN:
150602
Hom.:
46
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0529
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00582
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000885
Gnomad OTH
AF:
0.0126
GnomAD3 exomes
AF:
0.00399
AC:
996
AN:
249448
Hom.:
21
AF XY:
0.00298
AC XY:
402
AN XY:
134852
show subpopulations
Gnomad AFR exome
AF:
0.0546
Gnomad AMR exome
AF:
0.00232
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000166
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000124
Gnomad OTH exome
AF:
0.00230
GnomAD4 exome
AF:
0.00155
AC:
2246
AN:
1451096
Hom.:
46
Cov.:
34
AF XY:
0.00135
AC XY:
976
AN XY:
721852
show subpopulations
Gnomad4 AFR exome
AF:
0.0546
Gnomad4 AMR exome
AF:
0.00303
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000128
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000769
Gnomad4 OTH exome
AF:
0.00325
GnomAD4 genome
AF:
0.0153
AC:
2298
AN:
150684
Hom.:
48
Cov.:
31
AF XY:
0.0149
AC XY:
1093
AN XY:
73496
show subpopulations
Gnomad4 AFR
AF:
0.0532
Gnomad4 AMR
AF:
0.00581
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000885
Gnomad4 OTH
AF:
0.0124
Alfa
AF:
0.00758
Hom.:
13
Bravo
AF:
0.0174
Asia WGS
AF:
0.00549
AC:
19
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
CADD
Benign
4.5
DANN
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00011
dbscSNV1_RF
Benign
0.018
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: rs75440493; hg19: chr11-34135256; API