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GeneBe

2-38749547-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001031684.3(SRSF7):c.368G>A(p.Ser123Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SRSF7
NM_001031684.3 missense

Scores

1
6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.87
Variant links:
Genes affected
SRSF7 (HGNC:10789): (serine and arginine rich splicing factor 7) The protein encoded by this gene is a member of the serine/arginine (SR)-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. Each of these factors contains an N-terminal RNA recognition motif (RRM) for binding RNA and a C-terminal RS domain for binding other proteins. The RS domain is rich in serine and arginine residues and facilitates interaction between different SR splicing factors. In addition to being critical for mRNA splicing, the SR proteins have also been shown to be involved in mRNA export from the nucleus and in translation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2018]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2420741).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRSF7NM_001031684.3 linkuse as main transcriptc.368G>A p.Ser123Asn missense_variant 3/8 ENST00000313117.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRSF7ENST00000313117.11 linkuse as main transcriptc.368G>A p.Ser123Asn missense_variant 3/81 NM_001031684.3 P4Q16629-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

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 GeneticsOct 04, 2022The c.368G>A (p.S123N) alteration is located in exon 3 (coding exon 3) of the SRSF7 gene. This alteration results from a G to A substitution at nucleotide position 368, causing the serine (S) at amino acid position 123 to be replaced by an asparagine (N). 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
Uncertain
0.46
BayesDel_addAF
Uncertain
0.024
T
BayesDel_noAF
Benign
-0.20
CADD
Uncertain
25
DANN
Benign
0.97
DEOGEN2
Benign
0.044
T;.;.
Eigen
Uncertain
0.55
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Benign
0.82
T;T;T
M_CAP
Benign
0.066
D
MetaRNN
Benign
0.24
T;T;T
MetaSVM
Benign
-0.31
T
MutationAssessor
Benign
1.9
L;L;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Pathogenic
0.81
D
PROVEAN
Benign
-0.54
N;N;N
REVEL
Uncertain
0.32
Sift
Benign
0.46
T;T;T
Sift4G
Benign
0.097
T;T;T
Polyphen
0.98
D;.;.
Vest4
0.27
MutPred
0.28
Loss of phosphorylation at S123 (P = 5e-04);Loss of phosphorylation at S123 (P = 5e-04);Loss of phosphorylation at S123 (P = 5e-04);
MVP
0.59
MPC
1.6
ClinPred
0.82
D
GERP RS
6.0
Varity_R
0.22
gMVP
0.71

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-38976689; API