3-8634092-T-C

Variant names:

• chr3-8634092-T-C
• rs11131140
• NM_001256748.3:c.210-297A>G

Variant summary

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

The NM_001256748.3(SSUH2):​c.210-297A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 802,524 control chromosomes in the GnomAD database, including 243,868 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 0.77 (45489 hom., cov: 33)
  • Exomes 𝑓: 0.78 (198379 hom.)
• Consequence: SSUH2 NM_001256748.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256748.3. 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
	SSUH2	NM_001256748.3	MANE Select	c.210-297A>G		intron	N/A	NP_001243677.1	Q9Y2M2-2
	SSUH2	NM_001256749.3		c.-10-297A>G		intron	N/A	NP_001243678.1	Q9Y2M2-3
	SSUH2	NM_015931.4		c.-156-151A>G		intron	N/A	NP_057015.2	Q9Y2M2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSUH2	ENST00000544814.7	TSL:2 MANE Select	c.210-297A>G		intron	N/A	ENSP00000439378.1	Q9Y2M2-2
	SSUH2	ENST00000341795.7	TSL:1	c.-156-151A>G		intron	N/A	ENSP00000339150.4	Q9Y2M2-3
	SSUH2	ENST00000420394.5	TSL:1	c.-10-297A>G		intron	N/A	ENSP00000390328.2	F8WDV4

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117376 AN: 152120 Hom.: 45473 Cov.: 33

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.798

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.779

GnomAD4 exome AF: 0.780 AC: 507190 AN: 650286 Hom.: 198379 Cov.: 8 AF XY: 0.782 AC XY: 261352 AN XY: 334376

African (AFR) AF: 0.742 AC: 11943 AN: 16094

American (AMR) AF: 0.752 AC: 15301 AN: 20360

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 11580 AN: 15176

East Asian (EAS) AF: 0.853 AC: 27394 AN: 32122

South Asian (SAS) AF: 0.796 AC: 39566 AN: 49684

European-Finnish (FIN) AF: 0.845 AC: 26175 AN: 30982

Middle Eastern (MID) AF: 0.828 AC: 2359 AN: 2850

European-Non Finnish (NFE) AF: 0.772 AC: 347817 AN: 450380

Other (OTH) AF: 0.768 AC: 25055 AN: 32638

GnomAD4 genome AF: 0.771 AC: 117444 AN: 152238 Hom.: 45489 Cov.: 33 AF XY: 0.777 AC XY: 57857 AN XY: 74446

African (AFR) AF: 0.741 AC: 30797 AN: 41550

American (AMR) AF: 0.755 AC: 11546 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4187 AN: 5166

South Asian (SAS) AF: 0.795 AC: 3839 AN: 4826

European-Finnish (FIN) AF: 0.861 AC: 9131 AN: 10606

Middle Eastern (MID) AF: 0.800 AC: 232 AN: 290

European-Non Finnish (NFE) AF: 0.775 AC: 52698 AN: 68006

Other (OTH) AF: 0.774 AC: 1637 AN: 2114

Alfa AF: 0.772 Hom.: 79192

Bravo AF: 0.760

Asia WGS AF: 0.761 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11131140; hg19: chr3-8675778; COSMIC: COSV58030340; COSMIC: COSV58030340;