Genetic Variant ENST00000552085.1:c.129+5403C>A (chr12-95866696-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000552085.1(SNRPF):c.129+5403C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 159,660 control chromosomes in the GnomAD database, including 26,402 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 0.57 ( 25248 hom., cov: 33)

Exomes 𝑓: 0.54 ( 1154 hom. )

Consequence

SNRPF
ENST00000552085.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0300

Publications

5 publications found

Variant links:

Genes affected

SNRPF (HGNC:11162): (small nuclear ribonucleoprotein polypeptide F) Enables RNA binding activity. Involved in spliceosomal snRNP assembly. Located in cytosol and nucleus. Part of several cellular components, including methylosome; nucleus; and pICln-Sm protein complex. Biomarker of nasopharynx carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

SNRPF 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SNRPF	ENST00000552085.1 link	c.129+5403C>A	intron_variant	Intron 2 of 4	3	ENSP00000447127.1	F8W0W6
SNRPF	ENST00000553192.5 link	c.129+5403C>A	intron_variant	Intron 2 of 2	4	ENSP00000447751.1	A0A0B4J254
SNRPF	ENST00000549580.1 link	n.*245C>A	downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.572

AC:

86908

AN:

151864

Hom.:

25233

Cov.:

show subpopulations

Gnomad AFR

AF:

0.626

Gnomad AMI

AF:

0.522

Gnomad AMR

AF:

0.480

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.376

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.618

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.545

GnomAD4 exome

AF:

0.539

AC:

4138

AN:

7678

Hom.:

1154

Cov.:

AF XY:

0.541

AC XY:

2145

AN XY:

3962

show subpopulations

African (AFR)

AF:

0.618

AC:

147

AN:

238

American (AMR)

AF:

0.443

AC:

108

AN:

244

Ashkenazi Jewish (ASJ)

AF:

0.465

AC:

118

AN:

254

East Asian (EAS)

AF:

0.346

AC:

101

AN:

292

South Asian (SAS)

AF:

0.578

AC:

118

AN:

204

European-Finnish (FIN)

AF:

0.596

AC:

180

AN:

302

Middle Eastern (MID)

AF:

0.368

AC:

AN:

European-Non Finnish (NFE)

AF:

0.553

AC:

3105

AN:

5618

Other (OTH)

AF:

0.506

AC:

247

AN:

488

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

187

280

374

467

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.572

AC:

86965

AN:

151982

Hom.:

25248

Cov.:

AF XY:

0.572

AC XY:

42518

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.626

AC:

25946

AN:

41456

American (AMR)

AF:

0.479

AC:

7320

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.475

AC:

1647

AN:

3470

East Asian (EAS)

AF:

0.375

AC:

1940

AN:

5174

South Asian (SAS)

AF:

0.595

AC:

2869

AN:

4818

European-Finnish (FIN)

AF:

0.618

AC:

6522

AN:

10552

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.574

AC:

38957

AN:

67928

Other (OTH)

AF:

0.541

AC:

1141

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1919

3838

5756

7675

9594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<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:

0.576

Hom.:

10039

Bravo

AF:

0.564

Asia WGS

AF:

0.476

AC:

1655

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

(source)

DANN

Benign

0.40

PhyloP100

0.030

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over