rs5753073

Variant names:

• chr22-30332895-A-G
• rs5753073
• NM_005877.6:c.*1699T>C

Variant summary

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

The NM_005877.6(SF3A1):​c.*1699T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,224 control chromosomes in the GnomAD database, including 3,355 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 0.20 (3354 hom., cov: 32)
  • Exomes 𝑓: 0.19 (1 hom.)
• Consequence: SF3A1 NM_005877.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 12 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 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.*1699T>C		3_prime_UTR	Exon 16 of 16	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.*1699T>C		3_prime_UTR	Exon 16 of 16	ENSP00000215793.7	Q15459-1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30662 AN: 152064 Hom.: 3354 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.249

GnomAD4 exome AF: 0.190 AC: 8 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.206 AC XY: 7 AN XY: 34

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.219 AC: 7 AN: 32

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.201 AC: 30662 AN: 152182 Hom.: 3354 Cov.: 32 AF XY: 0.195 AC XY: 14490 AN XY: 74412

African (AFR) AF: 0.153 AC: 6339 AN: 41518

American (AMR) AF: 0.206 AC: 3150 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3468

East Asian (EAS) AF: 0.134 AC: 694 AN: 5184

South Asian (SAS) AF: 0.0976 AC: 470 AN: 4816

European-Finnish (FIN) AF: 0.156 AC: 1658 AN: 10598

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16456 AN: 67998

Other (OTH) AF: 0.246 AC: 519 AN: 2114

Alfa AF: 0.225 Hom.: 1961

Bravo AF: 0.206

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.8
DANN	Benign	0.82
PhyloP100		0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs5753073; hg19: chr22-30728884;