rs930863

Positions:

• chr12-131730255-C-A
• chr12-131730255-C-G
• chr12-131730255-C-T

Variant summary

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

The NM_004592.4(SFSWAP):​c.1081+1827C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,128 control chromosomes in the GnomAD database, including 22,133 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 0.52 (22133 hom., cov: 33)
• Consequence: SFSWAP NM_004592.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914

Genes affected

SFSWAP (HGNC:10790): (splicing factor SWAP) This gene encodes a human homolog of Drosophila splicing regulatory protein. This gene autoregulates its expression by control of splicing of its first two introns. In addition, it also regulates the splicing of fibronectin and CD45 genes. Two transcript variants encoding different isoforms have been identified. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFSWAP	NM_004592.4	c.1081+1827C>A		intron_variant		ENST00000261674.9	NP_004583.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFSWAP	ENST00000261674.9	c.1081+1827C>A		intron_variant		1	NM_004592.4	ENSP00000261674	P4

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78529 AN: 152010 Hom.: 22132 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.516 AC: 78543 AN: 152128 Hom.: 22133 Cov.: 33 AF XY: 0.525 AC XY: 39060 AN XY: 74360

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.509

Alfa AF: 0.547 Hom.: 2959

Bravo AF: 0.500

Asia WGS AF: 0.712 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.74

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: rs930863; hg19: chr12-132214800;