19-2241328-G-T

Position:

• chr19-2241328-G-T

Variant summary

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

The NM_007165.5(SF3A2):​c.-37-2054G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,008 control chromosomes in the GnomAD database, including 39,526 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 0.69 (39526 hom., cov: 31)
• Consequence: SF3A2 NM_007165.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SF3A2	NM_007165.5	c.-37-2054G>T		intron_variant		ENST00000221494.10	NP_009096.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SF3A2	ENST00000221494.10	c.-37-2054G>T		intron_variant		1	NM_007165.5	ENSP00000221494.3

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105610 AN: 151890 Hom.: 39539 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.695 AC: 105618 AN: 152008 Hom.: 39526 Cov.: 31 AF XY: 0.693 AC XY: 51475 AN XY: 74288

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.726

Alfa AF: 0.813 Hom.: 49924

Bravo AF: 0.670

Asia WGS AF: 0.547 AC: 1903 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.77

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: rs733846; hg19: chr19-2241327;