17-76736877-G-A

Position:

chr17-76736877-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM5PP5BP4BS2_Supporting

The NM_001195427.2(SRSF2):c.284C>T(p.Pro95Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000509 in 1,610,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P95R) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000047 ( 0 hom. )

Consequence

SRSF2
NM_001195427.2 missense

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:2

Conservation

PhyloP100: 7.00

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]

SRSF2 links:

MFSD11 (HGNC:25458): (major facilitator superfamily domain containing 11) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MFSD11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM5

Other missense variant is known to change same aminoacid residue: Variant chr17-76736877-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 998075.Status of the report is criteria_provided_single_submitter, 1 stars.

PP5

Variant 17-76736877-G-A is Pathogenic according to our data. Variant chr17-76736877-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 2504111.Status of the report is no_assertion_criteria_provided, 0 stars.

BP4

Computational evidence support a benign effect (MetaRNN=0.41523018). . Strength limited to SUPPORTING due to the PP5.

BS2

High AC in GnomAd4 at 14 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRSF2	NM_001195427.2 linkuse as main transcript	c.284C>T	p.Pro95Leu	missense_variant	1/3	ENST00000359995.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRSF2	ENST00000359995.10 linkuse as main transcript	c.284C>T	p.Pro95Leu	missense_variant	1/3	1	NM_001195427.2	P1	Q01130-1

Frequencies

GnomAD3 genomes

AF:

0.0000921

AC:

AN:

152068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000626

AC:

AN:

239480

Hom.:

AF XY:

0.0000910

AC XY:

AN XY:

131866

show subpopulations

Gnomad AFR exome

AF:

0.000141

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000102

Gnomad EAS exome

AF:

0.0000568

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000103

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000466

AC:

AN:

1458828

Hom.:

Cov.:

AF XY:

0.0000730

AC XY:

AN XY:

725590

show subpopulations

Gnomad4 AFR exome

AF:

0.0000598

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.0000384

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000522

Gnomad4 OTH exome

AF:

0.0000664

GnomAD4 genome

AF:

0.0000921

AC:

AN:

152068

Hom.:

Cov.:

AF XY:

0.000135

AC XY:

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.0000724

Gnomad4 AMR

AF:

0.0000654

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000132

Gnomad4 OTH

AF:

0.00

ExAC

AF:

0.0000832

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.000178

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Atypical chronic myeloid leukemia, BCR-ABL1 negative

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Institute of Laboratory Medicine, Hospital Wels-Grieskirchen

Apr 20, 2022

- -

Acute myeloid leukemia

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Sung Lab, Department of Medicine, Roswell Park Comprehensive Cancer Center

Jun 08, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.98

BayesDel_addAF

Benign

-0.17

BayesDel_noAF

Benign

-0.23

CADD

Pathogenic

DANN

Benign

0.97

DEOGEN2

Uncertain

0.44

T;T;.;.;T

Eigen

Benign

0.13

Eigen_PC

Benign

0.044

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.82

.;.;T;D;T

M_CAP

Pathogenic

0.97

MetaRNN

Benign

0.42

T;T;T;T;T

MetaSVM

Benign

-0.48

MutationAssessor

Uncertain

2.2

M;M;M;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D

PrimateAI

Pathogenic

0.92

PROVEAN

Pathogenic

-6.0

D;.;.;.;N

REVEL

Uncertain

0.36

Sift

Uncertain

0.0010

D;.;.;.;T

Sift4G

Benign

0.069

T;T;T;T;.

Polyphen

0.75

P;P;.;.;.

Vest4

0.44

MutPred

0.23

Loss of catalytic residue at P95 (P = 0.0376);Loss of catalytic residue at P95 (P = 0.0376);Loss of catalytic residue at P95 (P = 0.0376);Loss of catalytic residue at P95 (P = 0.0376);Loss of catalytic residue at P95 (P = 0.0376);

MVP

0.51

MPC

2.6

ClinPred

0.61

GERP RS

2.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.70

gMVP

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over