rs2684847

Variant names:

• chr18-47243946-C-A
• rs2684847
• NM_001278063.4:c.2752+962G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-47243946-C-A
• chr18-47243946-C-G
• chr18-47243946-C-T

Variant summary

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

The NM_001278063.4(SKOR2):​c.2752+962G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,190 control chromosomes in the GnomAD database, including 56,413 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 0.86 (56413 hom., cov: 32)
• Consequence: SKOR2 NM_001278063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SKOR2	NM_001278063.4	c.2752+962G>T		intron_variant	Intron 4 of 8	ENST00000425639.3	NP_001264992.1
SKOR2	NM_001037802.3	c.849+962G>T		intron_variant	Intron 3 of 3		NP_001032891.1
SKOR2	XM_047437757.1	c.2752+962G>T		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.2752+962G>T		intron_variant	Intron 4 of 8	5	NM_001278063.4	ENSP00000414750.3
SKOR2	ENST00000400404.1	c.849+962G>T		intron_variant	Intron 2 of 2	1		ENSP00000383255.1
SKOR2	ENST00000620245.4	c.2752+962G>T		intron_variant	Intron 3 of 6	5		ENSP00000483333.1

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130402 AN: 152072 Hom.: 56347 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.858 AC: 130527 AN: 152190 Hom.: 56413 Cov.: 32 AF XY: 0.860 AC XY: 64018 AN XY: 74404

African (AFR) AF: 0.960 AC: 39890 AN: 41546

American (AMR) AF: 0.839 AC: 12817 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2889 AN: 3470

East Asian (EAS) AF: 0.938 AC: 4865 AN: 5188

South Asian (SAS) AF: 0.845 AC: 4066 AN: 4810

European-Finnish (FIN) AF: 0.877 AC: 9278 AN: 10584

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53876 AN: 67990

Other (OTH) AF: 0.840 AC: 1775 AN: 2112

Alfa AF: 0.814 Hom.: 102163

Bravo AF: 0.861

Asia WGS AF: 0.887 AC: 3072 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.015
DANN	Benign	0.36
PhyloP100		-2.2
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: rs2684847; hg19: chr18-44770317;