11-34112124-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_024662.3(NAT10):​c.273C>T​(p.Asp91Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,614,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00046 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000036 ( 0 hom. )

Consequence

NAT10
NM_024662.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.82
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 Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 11-34112124-C-T is Benign according to our data. Variant chr11-34112124-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 732327.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.82 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NAT10NM_024662.3 linkc.273C>T p.Asp91Asp synonymous_variant Exon 4 of 29 ENST00000257829.8 NP_078938.3 Q9H0A0-1
NAT10NM_001144030.2 linkc.57C>T p.Asp19Asp synonymous_variant Exon 2 of 27 NP_001137502.2 Q9H0A0-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NAT10ENST00000257829.8 linkc.273C>T p.Asp91Asp synonymous_variant Exon 4 of 29 1 NM_024662.3 ENSP00000257829.3 Q9H0A0-1
NAT10ENST00000531159.6 linkc.57C>T p.Asp19Asp synonymous_variant Exon 2 of 27 2 ENSP00000433011.2 Q9H0A0-2
NAT10ENST00000527971.5 linkc.273C>T p.Asp91Asp synonymous_variant Exon 3 of 8 2 ENSP00000437324.1 E9PMU0
NAT10ENST00000529523.5 linkc.273C>T p.Asp91Asp synonymous_variant Exon 4 of 5 4 ENSP00000435569.1 E9PJN6

Frequencies

GnomAD3 genomes
AF:
0.000460
AC:
70
AN:
152196
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00150
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
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:
0.00
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.000103
AC:
26
AN:
251380
Hom.:
0
AF XY:
0.0000515
AC XY:
7
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.00148
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000356
AC:
52
AN:
1461888
Hom.:
0
Cov.:
31
AF XY:
0.0000358
AC XY:
26
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.00111
Gnomad4 AMR exome
AF:
0.000157
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000828
GnomAD4 genome
AF:
0.000460
AC:
70
AN:
152314
Hom.:
1
Cov.:
33
AF XY:
0.000389
AC XY:
29
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.00149
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.000526
Hom.:
0
Bravo
AF:
0.000586
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Feb 20, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely 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
-0.34
CADD
Benign
11
DANN
Benign
0.83

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

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

Other links and lift over

dbSNP: rs35401535; hg19: chr11-34133671; API