rs1045542

chr12-118417627-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022491.3(SUDS3):c.*3194G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 150,742 control chromosomes in the GnomAD database, including 590 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 0.073 (590 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: SUDS3 NM_022491.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUDS3	NM_022491.3	c.*3194G>A		3_prime_UTR_variant	12/12	ENST00000543473.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUDS3	ENST00000543473.2	c.*3194G>A		3_prime_UTR_variant	12/12	1	NM_022491.3	P1

Frequencies

GnomAD3 genomes AF: 0.0730 AC: 11002 AN: 150676 Hom.: 585 Cov.: 31

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.0853

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.0597

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0730 AC: 11009 AN: 150742 Hom.: 590 Cov.: 31 AF XY: 0.0750 AC XY: 5512 AN XY: 73540

Gnomad4 AFR AF: 0.0161

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.00156

Gnomad4 SAS AF: 0.0852

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0967

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.0783 Hom.: 129

Bravo AF: 0.0699

Asia WGS AF: 0.0360 AC: 126 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.3
Dann	Benign	0.74

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

Other links and lift over

dbSNP: rs1045542; hg19: chr12-118855432;