Genetic Variant SRSF11:n.1017G>A (chr1-70249410-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000461935.1(SRSF11):n.1017G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,280 control chromosomes in the GnomAD database, including 1,243 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1243 hom., cov: 32)

Exomes 𝑓: 0.074 ( 0 hom. )

Consequence

SRSF11
ENST00000461935.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546

Publications

2 publications found

Variant links:

Genes affected

SRSF11 (HGNC:10782): (serine and arginine rich splicing factor 11) This gene encodes 54-kD nuclear protein that contains an arginine/serine-rich region similar to segments found in pre-mRNA splicing factors. Although the function of this protein is not yet known, structure and immunolocalization data suggest that it may play a role in pre-mRNA processing. Alternative splicing results in multiple transcript variants encoding different proteins. In addition, a pseudogene of this gene has been found on chromosome 12.[provided by RefSeq, Sep 2010]

SRSF11 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRSF11	NM_001350605.2 link	c.1023-542G>A		intron_variant	Intron 9 of 11	ENST00000370949.2	NP_001337534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRSF11	ENST00000370949.2 link	c.1023-542G>A		intron_variant	Intron 9 of 11	1	NM_001350605.2	ENSP00000359987.2		Q05519-1Q5T757

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17805

AN:

151974

Hom.:

1225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.0722

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0815

Gnomad OTH

AF:

0.123

GnomAD4 exome

AF:

0.0745

AC:

AN:

188

Hom.:

Cov.:

AF XY:

0.0648

AC XY:

AN XY:

108

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.286

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0625

AC:

AN:

160

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.117

AC:

17867

AN:

152092

Hom.:

1243

Cov.:

AF XY:

0.121

AC XY:

8968

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.144

AC:

5976

AN:

41462

American (AMR)

AF:

0.152

AC:

2322

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

369

AN:

3470

East Asian (EAS)

AF:

0.303

AC:

1567

AN:

5170

South Asian (SAS)

AF:

0.200

AC:

966

AN:

4826

European-Finnish (FIN)

AF:

0.0722

AC:

764

AN:

10582

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0816

AC:

5546

AN:

67994

Other (OTH)

AF:

0.130

AC:

274

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

790

1581

2371

3162

3952

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.108

Hom.:

164

Bravo

AF:

0.123

Asia WGS

AF:

0.291

AC:

1011

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.18

(source)

DANN

Benign

0.66

PhyloP100

-0.55

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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chr1-70249410-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over