rs1107871

Variant names:

• chr12-131756114-A-G
• rs1107871
• NM_004592.4:c.1549-359A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SFSWAP	NM_004592.4	c.1549-359A>G		intron_variant	Intron 10 of 17	ENST00000261674.9	NP_004583.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFSWAP	ENST00000261674.9	c.1549-359A>G		intron_variant	Intron 10 of 17	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

African (AFR) AF: 0.322 AC: 13368 AN: 41520

American (AMR) AF: 0.489 AC: 7473 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2670 AN: 5146

South Asian (SAS) AF: 0.438 AC: 2114 AN: 4828

European-Finnish (FIN) AF: 0.503 AC: 5312 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30361 AN: 67980

Other (OTH) AF: 0.462 AC: 977 AN: 2114

Alfa AF: 0.417 Hom.: 1757

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
PhyloP100		-0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1107871; hg19: chr12-132240659;