chr12-118414120-C-T

Variant names:

• chr12-118414120-C-T
• rs7312555
• NM_022491.3:c.889-215C>T

Variant summary

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

The NM_022491.3(SUDS3):​c.889-215C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,136 control chromosomes in the GnomAD database, including 1,119 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 0.11 (1119 hom., cov: 32)
• Consequence: SUDS3 NM_022491.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUDS3	NM_022491.3	c.889-215C>T		intron_variant	Intron 11 of 11	ENST00000543473.2	NP_071936.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUDS3	ENST00000543473.2	c.889-215C>T		intron_variant	Intron 11 of 11	1	NM_022491.3	ENSP00000443988.1
SUDS3	ENST00000541280.1	n.608-215C>T		intron_variant	Intron 3 of 3	5
SUDS3	ENST00000541591.5	n.241-215C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16102 AN: 152018 Hom.: 1121 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.101

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.106 AC: 16095 AN: 152136 Hom.: 1119 Cov.: 32 AF XY: 0.105 AC XY: 7806 AN XY: 74380

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.00502

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0674 Hom.: 112

Bravo AF: 0.0971

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.070
DANN	Benign	0.59

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: rs7312555; hg19: chr12-118851925;