NM_005877.6:c.63+1092C>T

Variant names:

• chr22-30355638-G-A
• rs4820834
• NM_005877.6:c.63+1092C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005877.6(SF3A1):​c.63+1092C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0896 in 152,268 control chromosomes in the GnomAD database, including 817 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 0.090 (817 hom., cov: 32)
• Consequence: SF3A1 NM_005877.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 11 publications found

Genes affected

SF3A1 (HGNC:10765): (splicing factor 3a subunit 1) This gene encodes a subunit of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer is a component of the mature U2 small nuclear ribonucleoprotein particle (snRNP). U2 small nuclear ribonucleoproteins play a critical role in spliceosome assembly and pre-mRNA splicing. [provided by RefSeq, Aug 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005877.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SF3A1	NM_005877.6	MANE Select	c.63+1092C>T		intron	N/A	NP_005868.1	Q15459-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SF3A1	ENST00000215793.13	TSL:1 MANE Select	c.63+1092C>T		intron	N/A	ENSP00000215793.7	Q15459-1
	SF3A1	ENST00000872797.1		c.63+1092C>T		intron	N/A	ENSP00000542856.1
	SF3A1	ENST00000872796.1		c.63+1092C>T		intron	N/A	ENSP00000542855.1

Frequencies

GnomAD3 genomes AF: 0.0897 AC: 13648 AN: 152150 Hom.: 816 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0896 AC: 13649 AN: 152268 Hom.: 817 Cov.: 32 AF XY: 0.0861 AC XY: 6410 AN XY: 74458

African (AFR) AF: 0.0244 AC: 1014 AN: 41564

American (AMR) AF: 0.106 AC: 1629 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0263 AC: 127 AN: 4826

European-Finnish (FIN) AF: 0.0903 AC: 958 AN: 10606

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 9007 AN: 67998

Other (OTH) AF: 0.111 AC: 235 AN: 2112

Alfa AF: 0.110 Hom.: 468

Bravo AF: 0.0901

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.69
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4820834; hg19: chr22-30751627;