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

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000317371.8(SSUH2):​c.-608+3479G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,100 control chromosomes in the GnomAD database, including 3,517 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 0.20 (3517 hom., cov: 32)
• Consequence: SSUH2 ENST00000317371.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000317371.8. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSUH2	ENST00000317371.8	TSL:2	c.-608+3479G>A		intron	N/A	ENSP00000324551.5
	SSUH2	ENST00000435138.5	TSL:2	c.-485-3717G>A		intron	N/A	ENSP00000412333.2
	SSUH2	ENST00000455157.6	TSL:2	n.-883+3479G>A		intron	N/A	ENSP00000389937.3

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30241 AN: 151982 Hom.: 3510 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0516

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.199 AC: 30278 AN: 152100 Hom.: 3517 Cov.: 32 AF XY: 0.200 AC XY: 14843 AN XY: 74378

African (AFR) AF: 0.312 AC: 12951 AN: 41450

American (AMR) AF: 0.131 AC: 2006 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3472

East Asian (EAS) AF: 0.0517 AC: 268 AN: 5180

South Asian (SAS) AF: 0.159 AC: 766 AN: 4824

European-Finnish (FIN) AF: 0.234 AC: 2480 AN: 10576

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10522 AN: 67996

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.172 Hom.: 4991

Bravo AF: 0.197

Asia WGS AF: 0.139 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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;