rs2172557

Positions:

• chr3-8667519-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• 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/exons	MANE	UniProt
SSUH2	XM_017006511.2	c.-509+3479G>A		intron_variant
SSUH2	XM_017006512.2	c.-821+3479G>A		intron_variant
SSUH2	XM_017006513.2	c.-820-3608G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSUH2	ENST00000317371.8	c.-608+3479G>A		intron_variant		2
SSUH2	ENST00000435138.5	c.-485-3717G>A		intron_variant		2
SSUH2	ENST00000455157.6	c.-883+3479G>A		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.0517

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.184

Alfa AF: 0.160 Hom.: 2820

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2172557; hg19: chr3-8709205;