chr3-8629675-C-G

Variant names:

• chr3-8629675-C-G
• NM_001256748.3:c.577G>C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001256748.3(SSUH2):​c.577G>C​(p.Gly193Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000194 in 1,033,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 0.0000019 (0 hom.)
• Consequence: SSUH2 NM_001256748.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.67

Genes affected

SSUH2 (HGNC:24809): (ssu-2 homolog) Involved in odontogenesis. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.771

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSUH2	NM_001256748.3	c.577G>C	p.Gly193Arg	missense_variant	Exon 7 of 12	ENST00000544814.7	NP_001243677.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSUH2	ENST00000544814.7	c.577G>C	p.Gly193Arg	missense_variant	Exon 7 of 12	2	NM_001256748.3	ENSP00000439378.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 0.00000194 AC: 2 AN: 1033276 Hom.: 0 Cov.: 32 AF XY: 0.00000193 AC XY: 1 AN XY: 519068

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000265

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.62
BayesDel_addAF	Uncertain	0.058	T
BayesDel_noAF	Benign	-0.15
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.24	.;T;T
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.28
FATHMM_MKL	Benign	0.11	N
LIST_S2	Benign	0.85	T;.;D
M_CAP	Benign	0.036	D
MetaRNN	Pathogenic	0.77	D;D;D
MetaSVM	Benign	-0.52	T
MutationAssessor	Pathogenic	3.0	.;M;M
PrimateAI	Uncertain	0.52	T
PROVEAN	Pathogenic	-7.0	D;D;D
REVEL	Benign	0.29
Sift	Uncertain	0.0030	D;D;D
Sift4G	Uncertain	0.039	D;D;D
Polyphen		1.0	.;D;D
Vest4		0.63
MutPred		0.50		.;Gain of solvent accessibility (P = 6e-04);Gain of solvent accessibility (P = 6e-04);
MVP		0.38
MPC		0.35
ClinPred		0.98	D
GERP RS		4.7
Varity_R		0.69
gMVP		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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-8671361; COSMIC: COSV58030380; COSMIC: COSV58030380;