Genetic Variant SSUH2:c.210-297A>G (chr3-8634092-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.436

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSUH2	NM_001256748.3 link	c.210-297A>G		intron_variant	Intron 3 of 11	ENST00000544814.7	NP_001243677.1	Q9Y2M2-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSUH2	ENST00000544814.7 link	c.210-297A>G		intron_variant	Intron 3 of 11	2	NM_001256748.3	ENSP00000439378.1		Q9Y2M2-2

Frequencies

GnomAD3 genomes

AF:

0.772

AC:

117376

AN:

152120

Hom.:

45473

Cov.:

show subpopulations

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.:

AF XY:

0.782

AC XY:

261352

AN XY:

334376

show subpopulations

Gnomad4 AFR exome

AF:

0.742

Gnomad4 AMR exome

AF:

0.752

Gnomad4 ASJ exome

AF:

0.763

Gnomad4 EAS exome

AF:

0.853

Gnomad4 SAS exome

AF:

0.796

Gnomad4 FIN exome

AF:

0.845

Gnomad4 NFE exome

AF:

0.772

Gnomad4 OTH exome

AF:

0.768

GnomAD4 genome

AF:

0.771

AC:

117444

AN:

152238

Hom.:

45489

Cov.:

AF XY:

0.777

AC XY:

57857

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.741

Gnomad4 AMR

AF:

0.755

Gnomad4 ASJ

AF:

0.763

Gnomad4 EAS

AF:

0.810

Gnomad4 SAS

AF:

0.795

Gnomad4 FIN

AF:

0.861

Gnomad4 NFE

AF:

0.775

Gnomad4 OTH

AF:

0.774

Alfa

AF:

0.773

Hom.:

56103

Bravo

AF:

0.760

Asia WGS

AF:

0.761

AC:

2649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.8

DANN

Benign

0.78

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over