12-118414397-C-T

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_022491.3(SUDS3):​c.951C>T​(p.Arg317Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00583 in 1,602,612 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0049 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0059 ( 47 hom. )

Consequence

SUDS3
NM_022491.3 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.60
Variant links:
Genes affected
SUDS3 (HGNC:29545): (SDS3 homolog, SIN3A corepressor complex component) SDS3 is a subunit of the histone deacetylase (see HDAC1; MIM 601241)-dependent SIN3A (MIM 607776) corepressor complex (Fleischer et al., 2003 [PubMed 12724404]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 12-118414397-C-T is Benign according to our data. Variant chr12-118414397-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 791587.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.61 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 47 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SUDS3NM_022491.3 linkuse as main transcriptc.951C>T p.Arg317Arg synonymous_variant 12/12 ENST00000543473.2 NP_071936.2 Q9H7L9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SUDS3ENST00000543473.2 linkuse as main transcriptc.951C>T p.Arg317Arg synonymous_variant 12/121 NM_022491.3 ENSP00000443988.1 Q9H7L9
SUDS3ENST00000541591.5 linkuse as main transcriptn.303C>T non_coding_transcript_exon_variant 4/43
SUDS3ENST00000541280.1 linkuse as main transcriptn.*11C>T downstream_gene_variant 5

Frequencies

GnomAD3 genomes
AF:
0.00489
AC:
745
AN:
152218
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00101
Gnomad AMI
AF:
0.0296
Gnomad AMR
AF:
0.00530
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0137
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00654
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.00475
AC:
1085
AN:
228442
Hom.:
8
AF XY:
0.00460
AC XY:
567
AN XY:
123340
show subpopulations
Gnomad AFR exome
AF:
0.00103
Gnomad AMR exome
AF:
0.00163
Gnomad ASJ exome
AF:
0.00135
Gnomad EAS exome
AF:
0.000538
Gnomad SAS exome
AF:
0.000145
Gnomad FIN exome
AF:
0.0131
Gnomad NFE exome
AF:
0.00691
Gnomad OTH exome
AF:
0.00341
GnomAD4 exome
AF:
0.00593
AC:
8602
AN:
1450276
Hom.:
47
Cov.:
30
AF XY:
0.00577
AC XY:
4153
AN XY:
720212
show subpopulations
Gnomad4 AFR exome
AF:
0.000902
Gnomad4 AMR exome
AF:
0.00134
Gnomad4 ASJ exome
AF:
0.00108
Gnomad4 EAS exome
AF:
0.000408
Gnomad4 SAS exome
AF:
0.000191
Gnomad4 FIN exome
AF:
0.0130
Gnomad4 NFE exome
AF:
0.00681
Gnomad4 OTH exome
AF:
0.00402
GnomAD4 genome
AF:
0.00489
AC:
745
AN:
152336
Hom.:
1
Cov.:
32
AF XY:
0.00513
AC XY:
382
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.00101
Gnomad4 AMR
AF:
0.00530
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0137
Gnomad4 NFE
AF:
0.00654
Gnomad4 OTH
AF:
0.000945
Alfa
AF:
0.00544
Hom.:
3
Bravo
AF:
0.00373
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2023SUDS3: BP4, BP7, BS2 -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 20, 2017- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
0.93
DANN
Benign
0.63

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: rs147756379; hg19: chr12-118852202; COSMIC: COSV100820046; COSMIC: COSV100820046; API