Variant 1-23971864-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_054016.4(SRSF10):c.423G>A(p.Ser141Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000422 in 1,607,270 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00025 ( 1 hom. )

Consequence

SRSF10
NM_054016.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.139

Variant links:

Genes affected

SRSF10 (HGNC:16713): (serine and arginine rich splicing factor 10) This gene product is a member of the serine-arginine (SR) family of proteins, which are involved in constitutive and regulated RNA splicing. Members of this family are characterized by N-terminal RNP1 and RNP2 motifs, which are required for binding to RNA, and multiple C-terminal SR/RS repeats, which are important in mediating association with other cellular proteins. This protein interacts with the oncoprotein TLS, and abrogates the influence of TLS on adenovirus E1A pre-mRNA splicing. This gene has pseudogenes on chromosomes 4, 9, 14, 18, and 20. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

SRSF10 links:

SRSF10 (HGNC:):

SRSF10 links:

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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=-0.51).

BP6

Variant 1-23971864-C-T is Benign according to our data. Variant chr1-23971864-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638485.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.139 with no splicing effect.

BS2

High AC in GnomAd4 at 319 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRSF10	NM_054016.4 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/6	ENST00000492112.3	NP_473357.1	O75494-1A0A0S2Z504

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SRSF10	ENST00000492112.3 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/6	1	NM_054016.4	ENSP00000420195.1	O75494-1
SRSF10	ENST00000343255.9 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/6	2		ENSP00000344149.4	O75494-2
SRSF10	ENST00000344989.10 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/6	1		ENSP00000342913.5	O75494-3
SRSF10	ENST00000453840.7 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/6	1		ENSP00000388991.3	O75494-6
SRSF10	ENST00000374452.9 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/6	1		ENSP00000363576.5	O75494-4
SRSF10	ENST00000374453.7 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/6	5		ENSP00000363577.3	Q5JRI1
SRSF10	ENST00000484146.6 linkuse as main transcript	c.423G>A	p.Ser141Ser	synonymous_variant	4/5	2		ENSP00000419813.2	O75494-5

Frequencies

GnomAD3 genomes

AF:

0.00204

AC:

310

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00637

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.000827

AC:

AN:

29018

Hom.:

AF XY:

0.000825

AC XY:

AN XY:

15750

show subpopulations

Gnomad AFR exome

AF:

0.00618

Gnomad AMR exome

AF:

0.000177

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:

0.00

Gnomad OTH exome

AF:

0.00167

GnomAD4 exome

AF:

0.000247

AC:

359

AN:

1455020

Hom.:

Cov.:

AF XY:

0.000207

AC XY:

150

AN XY:

723896

show subpopulations

Gnomad4 AFR exome

AF:

0.00589

Gnomad4 AMR exome

AF:

0.000798

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0000471

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000550

Gnomad4 OTH exome

AF:

0.000982

GnomAD4 genome

AF:

0.00210

AC:

319

AN:

152250

Hom.:

Cov.:

AF XY:

0.00234

AC XY:

174

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00657

Gnomad4 AMR

AF:

0.00249

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000735

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.000285

Hom.:

Bravo

AF:

0.00233

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2022

SRSF10: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

8.5

DANN

Benign

0.73

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.

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