chr12-118417627-G-A

Variant names:

• chr12-118417627-G-A
• rs1045542
• NM_022491.3:c.*3194G>A

Variant summary

Our verdict is Benign. The variant received -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. Variant has been reported in ClinVar as (no stars).

• 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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022491.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUDS3	NM_022491.3	MANE Select	c.*3194G>A		3_prime_UTR	Exon 12 of 12	NP_071936.2	Q9H7L9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUDS3	ENST00000543473.2	TSL:1 MANE Select	c.*3194G>A		3_prime_UTR	Exon 12 of 12	ENSP00000443988.1	Q9H7L9
	SUDS3	ENST00000859515.1		c.*3194G>A		3_prime_UTR	Exon 11 of 11	ENSP00000529574.1
	SUDS3	ENST00000859516.1		c.*3194G>A		3_prime_UTR	Exon 11 of 11	ENSP00000529575.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0161 AC: 663 AN: 41064

American (AMR) AF: 0.116 AC: 1763 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3462

East Asian (EAS) AF: 0.00156 AC: 8 AN: 5122

South Asian (SAS) AF: 0.0852 AC: 403 AN: 4728

European-Finnish (FIN) AF: 0.122 AC: 1236 AN: 10150

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0967 AC: 6551 AN: 67762

Other (OTH) AF: 0.0588 AC: 122 AN: 2076

Alfa AF: 0.0707 Hom.: 335

Bravo AF: 0.0699

Asia WGS AF: 0.0360 AC: 126 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.3
DANN	Benign	0.74
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1045542; hg19: chr12-118855432;