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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSUH2	XM_017006511.2	c.-509+3479G>A		intron_variant	Intron 4 of 19		XP_016862000.1
SSUH2	XM_017006512.2	c.-821+3479G>A		intron_variant	Intron 3 of 19		XP_016862001.1
SSUH2	XM_017006513.2	c.-820-3608G>A		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>A		intron_variant	Intron 5 of 18	2		ENSP00000324551.5
SSUH2	ENST00000435138.5	c.-485-3717G>A		intron_variant	Intron 5 of 17	2		ENSP00000412333.2
SSUH2	ENST00000455157.6	n.-883+3479G>A		intron_variant	Intron 2 of 16	2		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 v4.3

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;