rs1107871

Positions:

• chr12-131756114-A-G
• chr12-131756114-A-T

Variant summary

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

The NM_004592.4(SFSWAP):​c.1549-359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,098 control chromosomes in the GnomAD database, including 14,020 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 0.42 (14020 hom., cov: 33)
• Consequence: SFSWAP NM_004592.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

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]

SFSWAP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFSWAP	NM_004592.4	c.1549-359A>G		intron_variant		ENST00000261674.9	NP_004583.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFSWAP	ENST00000261674.9	c.1549-359A>G		intron_variant		1	NM_004592.4	ENSP00000261674.4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64348 AN: 151980 Hom.: 14001 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.423 AC: 64413 AN: 152098 Hom.: 14020 Cov.: 33 AF XY: 0.430 AC XY: 31932 AN XY: 74344

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.462

Alfa AF: 0.420 Hom.: 1716

Bravo AF: 0.421

Asia WGS AF: 0.481 AC: 1670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1107871; hg19: chr12-132240659;