dbSNP rs4807216: SF3A2:c.*138C>T (chr19-2248684-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007165.5(SF3A2):c.*138C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 380,430 control chromosomes in the GnomAD database, including 122,508 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 0.76 ( 44897 hom., cov: 26)

Exomes 𝑓: 0.82 ( 77611 hom. )

Consequence

SF3A2
NM_007165.5 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.623

Variant links:

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]

SF3A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SF3A2	NM_007165.5 link	c.*138C>T		downstream_gene_variant		ENST00000221494.10	NP_009096.2	Q15428Q05DF2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SF3A2	ENST00000221494.10 link	c.*138C>T		downstream_gene_variant		1	NM_007165.5	ENSP00000221494.3		Q15428

Frequencies

GnomAD3 genomes

AF:

0.761

AC:

114843

AN:

150934

Hom.:

44899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.581

Gnomad AMI

AF:

0.857

Gnomad AMR

AF:

0.759

Gnomad ASJ

AF:

0.894

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.800

Gnomad FIN

AF:

0.830

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.859

Gnomad OTH

AF:

0.791

GnomAD4 exome

AF:

0.817

AC:

187323

AN:

229378

Hom.:

77611

Cov.:

AF XY:

0.818

AC XY:

94920

AN XY:

116014

show subpopulations

Gnomad4 AFR exome

AF:

0.583

Gnomad4 AMR exome

AF:

0.716

Gnomad4 ASJ exome

AF:

0.885

Gnomad4 EAS exome

AF:

0.626

Gnomad4 SAS exome

AF:

0.788

Gnomad4 FIN exome

AF:

0.823

Gnomad4 NFE exome

AF:

0.855

Gnomad4 OTH exome

AF:

0.803

GnomAD4 genome

AF:

0.761

AC:

114878

AN:

151052

Hom.:

44897

Cov.:

AF XY:

0.760

AC XY:

56094

AN XY:

73806

show subpopulations

Gnomad4 AFR

AF:

0.581

Gnomad4 AMR

AF:

0.759

Gnomad4 ASJ

AF:

0.894

Gnomad4 EAS

AF:

0.608

Gnomad4 SAS

AF:

0.799

Gnomad4 FIN

AF:

0.830

Gnomad4 NFE

AF:

0.859

Gnomad4 OTH

AF:

0.784

Alfa

AF:

0.789

Hom.:

4488

Bravo

AF:

0.742

Asia WGS

AF:

0.651

AC:

2268

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.9

DANN

Benign

0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over