rs2684847

chr18-47243946-C-Achr18-47243946-C-Gchr18-47243946-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SKOR2	NM_001278063.4	c.2752+962G>T		intron_variant		ENST00000425639.3
SKOR2	NM_001037802.3	c.849+962G>T		intron_variant
SKOR2	XM_047437757.1	c.2752+962G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SKOR2	ENST00000425639.3	c.2752+962G>T		intron_variant		5	NM_001278063.4	P1
SKOR2	ENST00000400404.1	c.849+962G>T		intron_variant		1
SKOR2	ENST00000620245.4	c.2752+962G>T		intron_variant		5		P1

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

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.840

Alfa AF: 0.802 Hom.: 65708

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

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

Other links and lift over

dbSNP: rs2684847; hg19: chr18-44770317;