rs350808

Variant names:

• chr3-8685092-G-A
• rs350808
• ENST00000435138.5:c.-633-7739C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-8685092-G-A
• chr3-8685092-G-T

Variant summary

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

The ENST00000435138.5(SSUH2):​c.-633-7739C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 150,568 control chromosomes in the GnomAD database, including 54 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 0.022 (54 hom., cov: 31)
• Consequence: SSUH2 ENST00000435138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• 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

ENSG00000291007 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0523 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	ENST00000435138.5	c.-633-7739C>T		intron_variant	Intron 4 of 17	2		ENSP00000412333.2
ENSG00000291007	ENST00000641144.1	n.651+1352G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3358 AN: 150446 Hom.: 53 Cov.: 31

Gnomad AFR AF: 0.00517

Gnomad AMI AF: 0.0413

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0325

Gnomad OTH AF: 0.0217

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

GnomAD4 genome AF: 0.0223 AC: 3360 AN: 150568 Hom.: 54 Cov.: 31 AF XY: 0.0220 AC XY: 1619 AN XY: 73560

African (AFR) AF: 0.00516 AC: 211 AN: 40922

American (AMR) AF: 0.0140 AC: 212 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 255 AN: 3454

East Asian (EAS) AF: 0.00 AC: 0 AN: 5096

South Asian (SAS) AF: 0.0580 AC: 274 AN: 4728

European-Finnish (FIN) AF: 0.0118 AC: 124 AN: 10474

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0325 AC: 2192 AN: 67442

Other (OTH) AF: 0.0215 AC: 45 AN: 2094

Alfa AF: 0.0262 Hom.: 7

Bravo AF: 0.0198

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.60
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs350808; hg19: chr3-8726778;