rs9304344

Variant names:

• chr18-47232294-G-C
• rs9304344
• NM_001278063.4:c.2753-1294C>G

Your query was ambiguous. Multiple possible variants found:

• chr18-47232294-G-C
• chr18-47232294-G-T

Variant summary

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

The NM_001278063.4(SKOR2):​c.2753-1294C>G 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: 32)
• Consequence: SKOR2 NM_001278063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 4 publications found

Genes affected

SKOR2 (HGNC:32695): (SKI family transcriptional corepressor 2) Enables SMAD binding activity and sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transforming growth factor beta receptor signaling pathway. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SKOR2 Gene-Disease associations (from GenCC):

• nervous system disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SKOR2	NM_001278063.4	c.2753-1294C>G		intron_variant	Intron 4 of 8	ENST00000425639.3	NP_001264992.1
SKOR2	NM_001037802.3	c.850-1130C>G		intron_variant	Intron 3 of 3		NP_001032891.1
SKOR2	XM_047437757.1	c.2753-1294C>G		intron_variant	Intron 3 of 7		XP_047293713.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SKOR2	ENST00000425639.3	c.2753-1294C>G		intron_variant	Intron 4 of 8	5	NM_001278063.4	ENSP00000414750.3
SKOR2	ENST00000400404.1	c.850-1130C>G		intron_variant	Intron 2 of 2	1		ENSP00000383255.1
SKOR2	ENST00000620245.4	c.2753-1294C>G		intron_variant	Intron 3 of 6	5		ENSP00000483333.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2543

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.51
PhyloP100		-0.65

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: rs9304344; hg19: chr18-44758665;