ENST00000317371.8:c.-608+3479G>T

Variant names:

• chr3-8667519-C-A
• rs2172557
• ENST00000317371.8:c.-608+3479G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000317371.8(SSUH2):​c.-608+3479G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SSUH2 ENST00000317371.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 0 publications found

Genes affected

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

SSUH2 Gene-Disease associations (from GenCC):

• dentin dysplasia type I

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSUH2	XM_017006511.2	c.-509+3479G>T		intron_variant	Intron 4 of 19		XP_016862000.1
SSUH2	XM_017006512.2	c.-821+3479G>T		intron_variant	Intron 3 of 19		XP_016862001.1
SSUH2	XM_017006513.2	c.-820-3608G>T		intron_variant	Intron 2 of 18		XP_016862002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSUH2	ENST00000317371.8	c.-608+3479G>T		intron_variant	Intron 5 of 18	2		ENSP00000324551.5
SSUH2	ENST00000435138.5	c.-485-3717G>T		intron_variant	Intron 5 of 17	2		ENSP00000412333.2
SSUH2	ENST00000455157.6	n.-883+3479G>T		intron_variant	Intron 2 of 16	2		ENSP00000389937.3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2172557; hg19: chr3-8709205;