3-8634092-T-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001256748.3(SSUH2):​c.210-297A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

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>C		intron	N/A	NP_001243677.1	Q9Y2M2-2
	SSUH2	NM_001256749.3		c.-10-297A>C		intron	N/A	NP_001243678.1	Q9Y2M2-3
	SSUH2	NM_015931.4		c.-156-151A>C		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>C		intron	N/A	ENSP00000439378.1	Q9Y2M2-2
	SSUH2	ENST00000341795.7	TSL:1	c.-156-151A>C		intron	N/A	ENSP00000339150.4	Q9Y2M2-3
	SSUH2	ENST00000420394.5	TSL:1	c.-10-297A>C		intron	N/A	ENSP00000390328.2	F8WDV4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 651064 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 334766

African (AFR) AF: 0.00 AC: 0 AN: 16120

American (AMR) AF: 0.00 AC: 0 AN: 20362

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15190

East Asian (EAS) AF: 0.00 AC: 0 AN: 32130

South Asian (SAS) AF: 0.00 AC: 0 AN: 49712

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31004

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2856

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 451026

Other (OTH) AF: 0.00 AC: 0 AN: 32664

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.78
PhyloP100		-0.44

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;