rs7249235

Positions:

• chr19-2242830-A-C
• chr19-2242830-A-T

Variant summary

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

The ENST00000221494.10(SF3A2):​c.-37-552A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,072 control chromosomes in the GnomAD database, including 55,571 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 0.85 (55571 hom., cov: 31)
• Consequence: SF3A2 ENST00000221494.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

SF3A2 (HGNC:10766): (splicing factor 3a subunit 2) This gene encodes subunit 2 of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer includes subunits 1, 2 and 3 and is necessary for the in vitro conversion of 15S U2 snRNP into an active 17S particle that performs pre-mRNA splicing. Subunit 2 interacts with subunit 1 through its amino-terminus while the single zinc finger domain of subunit 2 plays a role in its binding to the 15S U2 snRNP. Subunit 2 may also function independently of its RNA splicing function as a microtubule-binding protein. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SF3A2	NM_007165.5	c.-37-552A>C		intron_variant		ENST00000221494.10	NP_009096.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SF3A2	ENST00000221494.10	c.-37-552A>C		intron_variant		1	NM_007165.5	ENSP00000221494	P1

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129332 AN: 151954 Hom.: 55552 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.851 AC: 129400 AN: 152072 Hom.: 55571 Cov.: 31 AF XY: 0.852 AC XY: 63381 AN XY: 74400

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.868

Alfa AF: 0.896 Hom.: 73478

Bravo AF: 0.836

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.046
DANN	Benign	0.30

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: rs7249235; hg19: chr19-2242829;