3-8714737-G-C

Variant names:

• chr3-8714737-G-C
• rs17788626
• ENST00000478513.1:n.620+865C>G

Variant summary

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

The ENST00000435138.5(SSUH2):​c.-841+865C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 152,292 control chromosomes in the GnomAD database, including 235 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 0.046 (235 hom., cov: 32)
• Consequence: SSUH2 ENST00000435138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSUH2	ENST00000478513.1	n.620+865C>G		intron_variant	Intron 3 of 4	1
SSUH2	ENST00000435138.5	c.-841+865C>G		intron_variant	Intron 3 of 17	2		ENSP00000412333.2

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7047 AN: 152174 Hom.: 236 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0506

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0462 AC: 7040 AN: 152292 Hom.: 235 Cov.: 32 AF XY: 0.0457 AC XY: 3405 AN XY: 74470

Gnomad4 AFR AF: 0.0115

Gnomad4 AMR AF: 0.0259

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0496

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0710

Gnomad4 OTH AF: 0.0340

Alfa AF: 0.0528 Hom.: 26

Bravo AF: 0.0407

Asia WGS AF: 0.0160 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17788626; hg19: chr3-8756423;