chr18-47239098-G-A

Position:

• chr18-47239098-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278063.4(SKOR2):​c.2752+5810C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,016 control chromosomes in the GnomAD database, including 11,137 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 0.37 (11137 hom., cov: 33)
• Consequence: SKOR2 NM_001278063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SKOR2	NM_001278063.4	c.2752+5810C>T		intron_variant		ENST00000425639.3	NP_001264992.1
SKOR2	NM_001037802.3	c.849+5810C>T		intron_variant			NP_001032891.1
SKOR2	XM_047437757.1	c.2752+5810C>T		intron_variant			XP_047293713.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SKOR2	ENST00000425639.3	c.2752+5810C>T		intron_variant		5	NM_001278063.4	ENSP00000414750	P1
SKOR2	ENST00000400404.1	c.849+5810C>T		intron_variant		1		ENSP00000383255
SKOR2	ENST00000620245.4	c.2752+5810C>T		intron_variant		5		ENSP00000483333	P1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56525 AN: 151898 Hom.: 11133 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.372 AC: 56534 AN: 152016 Hom.: 11137 Cov.: 33 AF XY: 0.375 AC XY: 27857 AN XY: 74288

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.380

Alfa AF: 0.389 Hom.: 2028

Bravo AF: 0.357

Asia WGS AF: 0.264 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.97
DANN	Benign	0.34

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: rs17785419; hg19: chr18-44765469;