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GeneBe

17-76737017-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001195427.2(SRSF2):c.144C>T(p.Asp48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 1,613,358 control chromosomes in the GnomAD database, including 670,295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.81 ( 52442 hom., cov: 35)
Exomes 𝑓: 0.92 ( 617853 hom. )

Consequence

SRSF2
NM_001195427.2 synonymous

Scores

1
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.15
Variant links:
Genes affected
SRSF2 (HGNC:10783): (serine and arginine rich splicing factor 2) 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 RNA recognition motif (RRM) for binding RNA and an 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. Two transcript variants encoding the same protein and one non-coding transcript variant have been found for this gene. In addition, a pseudogene of this gene has been found on chromosome 11. [provided by RefSeq, Sep 2010]
MFSD11 (HGNC:25458): (major facilitator superfamily domain containing 11) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 17-76737017-G-A is Benign according to our data. Variant chr17-76737017-G-A is described in ClinVar as [Benign]. Clinvar id is 3058855.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.15 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRSF2NM_001195427.2 linkuse as main transcriptc.144C>T p.Asp48= synonymous_variant 1/3 ENST00000359995.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRSF2ENST00000359995.10 linkuse as main transcriptc.144C>T p.Asp48= synonymous_variant 1/31 NM_001195427.2 P1Q01130-1

Frequencies

GnomAD3 genomes
AF:
0.809
AC:
123008
AN:
152112
Hom.:
52437
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.511
Gnomad AMI
AF:
0.995
Gnomad AMR
AF:
0.887
Gnomad ASJ
AF:
0.958
Gnomad EAS
AF:
0.920
Gnomad SAS
AF:
0.919
Gnomad FIN
AF:
0.894
Gnomad MID
AF:
0.892
Gnomad NFE
AF:
0.931
Gnomad OTH
AF:
0.838
GnomAD3 exomes
AF:
0.895
AC:
222037
AN:
248222
Hom.:
100689
AF XY:
0.903
AC XY:
121849
AN XY:
134980
show subpopulations
Gnomad AFR exome
AF:
0.498
Gnomad AMR exome
AF:
0.912
Gnomad ASJ exome
AF:
0.952
Gnomad EAS exome
AF:
0.923
Gnomad SAS exome
AF:
0.915
Gnomad FIN exome
AF:
0.891
Gnomad NFE exome
AF:
0.929
Gnomad OTH exome
AF:
0.917
GnomAD4 exome
AF:
0.917
AC:
1340100
AN:
1461128
Hom.:
617853
Cov.:
85
AF XY:
0.919
AC XY:
667668
AN XY:
726890
show subpopulations
Gnomad4 AFR exome
AF:
0.502
Gnomad4 AMR exome
AF:
0.910
Gnomad4 ASJ exome
AF:
0.951
Gnomad4 EAS exome
AF:
0.910
Gnomad4 SAS exome
AF:
0.916
Gnomad4 FIN exome
AF:
0.891
Gnomad4 NFE exome
AF:
0.932
Gnomad4 OTH exome
AF:
0.899
GnomAD4 genome
AF:
0.808
AC:
123053
AN:
152230
Hom.:
52442
Cov.:
35
AF XY:
0.811
AC XY:
60362
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.511
Gnomad4 AMR
AF:
0.887
Gnomad4 ASJ
AF:
0.958
Gnomad4 EAS
AF:
0.920
Gnomad4 SAS
AF:
0.919
Gnomad4 FIN
AF:
0.894
Gnomad4 NFE
AF:
0.931
Gnomad4 OTH
AF:
0.840
Alfa
AF:
0.901
Hom.:
70864
Bravo
AF:
0.793
Asia WGS
AF:
0.882
AC:
3066
AN:
3478
EpiCase
AF:
0.935
EpiControl
AF:
0.933

ClinVar

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

Submissions by phenotype

SRSF2-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesMay 03, 2022This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
13
DANN
Uncertain
0.98

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: rs237057; hg19: chr17-74733099; API