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GeneBe

20-43460203-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_006275.6(SRSF6):c.552C>T(p.Arg184=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 1,613,988 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0036 ( 19 hom. )

Consequence

SRSF6
NM_006275.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.382
Variant links:
Genes affected
SRSF6 (HGNC:10788): (serine and arginine rich splicing factor 6) The protein encoded by this gene is involved in mRNA splicing and may play a role in the determination of alternative splicing. The encoded nuclear protein belongs to the splicing factor SR family and has been shown to bind with and modulate another member of the family, SFRS12. Alternative splicing results in multiple transcript variants. In addition, two pseudogenes, one on chromosome 17 and the other on the X chromosome, have been found for this gene.[provided by RefSeq, Sep 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 20-43460203-C-T is Benign according to our data. Variant chr20-43460203-C-T is described in ClinVar as [Benign]. Clinvar id is 731744.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.382 with no splicing effect.
BS2
High AC in GnomAd4 at 420 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRSF6NM_006275.6 linkuse as main transcriptc.552C>T p.Arg184= synonymous_variant 4/6 ENST00000244020.5
SRSF6NR_034009.2 linkuse as main transcriptn.958C>T non_coding_transcript_exon_variant 5/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRSF6ENST00000244020.5 linkuse as main transcriptc.552C>T p.Arg184= synonymous_variant 4/61 NM_006275.6 P2Q13247-1

Frequencies

GnomAD3 genomes
AF:
0.00276
AC:
420
AN:
152186
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000700
Gnomad AMI
AF:
0.0702
Gnomad AMR
AF:
0.00144
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00104
Gnomad FIN
AF:
0.00264
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00391
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00272
AC:
678
AN:
249384
Hom.:
1
AF XY:
0.00273
AC XY:
370
AN XY:
135410
show subpopulations
Gnomad AFR exome
AF:
0.000647
Gnomad AMR exome
AF:
0.00136
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00114
Gnomad FIN exome
AF:
0.00381
Gnomad NFE exome
AF:
0.00431
Gnomad OTH exome
AF:
0.00297
GnomAD4 exome
AF:
0.00359
AC:
5253
AN:
1461684
Hom.:
19
Cov.:
33
AF XY:
0.00354
AC XY:
2571
AN XY:
727148
show subpopulations
Gnomad4 AFR exome
AF:
0.000568
Gnomad4 AMR exome
AF:
0.00141
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00121
Gnomad4 FIN exome
AF:
0.00345
Gnomad4 NFE exome
AF:
0.00423
Gnomad4 OTH exome
AF:
0.00283
GnomAD4 genome
AF:
0.00276
AC:
420
AN:
152304
Hom.:
1
Cov.:
33
AF XY:
0.00246
AC XY:
183
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.000698
Gnomad4 AMR
AF:
0.00144
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.00264
Gnomad4 NFE
AF:
0.00391
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00306
Hom.:
1
Bravo
AF:
0.00286

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
8.6
DANN
Benign
0.49
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs141443913; hg19: chr20-42088843; API