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GeneBe

1-29148602-A-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 3P and 8B. PM1PP2BP4_StrongBS2

The NM_005626.5(SRSF4):c.1293T>A(p.Ser431Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000651 in 1,613,324 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000065 ( 0 hom. )

Consequence

SRSF4
NM_005626.5 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.917
Variant links:
Genes affected
SRSF4 (HGNC:10786): (serine and arginine rich splicing factor 4) Enables RNA binding activity. Involved in negative regulation of mRNA splicing, via spliceosome. Located in nuclear speck. Biomarker of Down syndrome; acute myeloid leukemia; clear cell renal cell carcinoma; and colon adenocarcinoma. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM1
In a modified_residue Phosphoserine (size 0) in uniprot entity SRSF4_HUMAN
PP2
Missense variant where missense usually causes diseases, SRSF4
BP4
Computational evidence support a benign effect (MetaRNN=0.035991818).
BS2
High AC in GnomAd4 at 10 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRSF4NM_005626.5 linkuse as main transcriptc.1293T>A p.Ser431Arg missense_variant 6/6 ENST00000373795.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRSF4ENST00000373795.7 linkuse as main transcriptc.1293T>A p.Ser431Arg missense_variant 6/61 NM_005626.5 P1
SRSF4ENST00000634348.1 linkuse as main transcriptn.7379T>A non_coding_transcript_exon_variant 7/75
SRSF4ENST00000691479.1 linkuse as main transcriptc.*1500T>A 3_prime_UTR_variant, NMD_transcript_variant 10/10

Frequencies

GnomAD3 genomes
AF:
0.0000660
AC:
10
AN:
151552
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000146
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000589
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000557
AC:
14
AN:
251374
Hom.:
0
AF XY:
0.0000662
AC XY:
9
AN XY:
135858
show subpopulations
Gnomad AFR exome
AF:
0.000123
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000967
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000650
AC:
95
AN:
1461772
Hom.:
0
Cov.:
29
AF XY:
0.0000564
AC XY:
41
AN XY:
727162
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000791
Gnomad4 OTH exome
AF:
0.0000994
GnomAD4 genome
AF:
0.0000660
AC:
10
AN:
151552
Hom.:
0
Cov.:
32
AF XY:
0.0000406
AC XY:
3
AN XY:
73970
show subpopulations
Gnomad4 AFR
AF:
0.000146
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000589
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000282
Hom.:
0
Bravo
AF:
0.0000604
ExAC
AF:
0.0000659
AC:
8

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 05, 2022The c.1293T>A (p.S431R) alteration is located in exon 6 (coding exon 6) of the SRSF4 gene. This alteration results from a T to A substitution at nucleotide position 1293, causing the serine (S) at amino acid position 431 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
12
DANN
Uncertain
0.98
DEOGEN2
Benign
0.0067
T
Eigen
Benign
-0.63
Eigen_PC
Benign
-0.55
FATHMM_MKL
Benign
0.45
N
LIST_S2
Benign
0.63
T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.036
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-0.34
N
MutationTaster
Benign
1.0
D;N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-0.27
N
REVEL
Benign
0.051
Sift
Uncertain
0.022
D
Sift4G
Benign
0.39
T
Polyphen
0.0030
B
Vest4
0.22
MutPred
0.30
Loss of phosphorylation at S431 (P = 0.0011);
MVP
0.27
MPC
0.25
ClinPred
0.042
T
GERP RS
0.20
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.063
gMVP
0.42

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

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

Other links and lift over

dbSNP: rs767598320; hg19: chr1-29475114; API