dbSNP rs3767206: 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461935.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SRSF11	NM_001350605.2	MANE Select	c.1023-542G>A	intron	N/A	NP_001337534.1
SRSF11	NM_001394402.1		c.1056-542G>A	intron	N/A	NP_001381331.1
SRSF11	NM_001394403.1		c.1056-542G>A	intron	N/A	NP_001381332.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SRSF11	ENST00000461935.1	TSL:1	n.1017G>A	non_coding_transcript_exon	Exon 1 of 2
SRSF11	ENST00000370949.2	TSL:1 MANE Select	c.1023-542G>A	intron	N/A	ENSP00000359987.2
SRSF11	ENST00000395136.7	TSL:1	c.1023-521G>A	intron	N/A	ENSP00000378568.3

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

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over