ENST00000478513.1:n.621-3730C>T

Variant names:

• chr3-8706962-G-A
• rs164462
• ENST00000478513.1:n.621-3730C>T

Variant summary

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

The ENST00000478513.1(SSUH2):​n.621-3730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,750 control chromosomes in the GnomAD database, including 22,131 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 0.53 (22131 hom., cov: 30)
• Consequence: SSUH2 ENST00000478513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 2 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 = 0.672 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	ENST00000478513.1	n.621-3730C>T		intron_variant	Intron 3 of 4	1
SSUH2	ENST00000435138.5	c.-840-3730C>T		intron_variant	Intron 3 of 17	2		ENSP00000412333.2

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79659 AN: 151632 Hom.: 22092 Cov.: 30

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.526 AC: 79765 AN: 151750 Hom.: 22131 Cov.: 30 AF XY: 0.523 AC XY: 38799 AN XY: 74146

African (AFR) AF: 0.679 AC: 28096 AN: 41372

American (AMR) AF: 0.613 AC: 9353 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1721 AN: 3464

East Asian (EAS) AF: 0.589 AC: 3023 AN: 5136

South Asian (SAS) AF: 0.393 AC: 1884 AN: 4796

European-Finnish (FIN) AF: 0.381 AC: 4014 AN: 10538

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30057 AN: 67896

Other (OTH) AF: 0.542 AC: 1142 AN: 2108

Alfa AF: 0.473 Hom.: 67676

Bravo AF: 0.556

Asia WGS AF: 0.510 AC: 1774 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	0.11
DANN	Benign	0.40
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs164462; hg19: chr3-8748648;