dbSNP rs10493066: SFPQ:n.122G>A (chr1-35180524-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000468598.5(SFPQ):n.122G>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 0.0724 in 1,049,484 control chromosomes in the GnomAD database, including 16,290 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 0.23 ( 8834 hom., cov: 32)

Exomes 𝑓: 0.045 ( 7456 hom. )

Consequence

SFPQ
ENST00000468598.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.152

Publications

6 publications found

Variant links:

Genes affected

SFPQ (HGNC:10774): (splicing factor proline and glutamine rich) Enables DNA binding activity; histone deacetylase binding activity; and protein homodimerization activity. Involved in several processes, including alternative mRNA splicing, via spliceosome; positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway; and regulation of transcription by RNA polymerase II. Acts upstream of or within double-strand break repair via homologous recombination. Located in chromatin; nuclear matrix; and paraspeckles. [provided by Alliance of Genome Resources, Apr 2022]

SFPQ 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=-0.72).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
SFPQ	XM_017002053.3 link	c.*3932G>A	3_prime_UTR_variant	Exon 10 of 12	XP_016857542.1	P23246-1A0A384N5Z8
SFPQ	XM_017002054.3 link	c.*3932G>A	3_prime_UTR_variant	Exon 10 of 12	XP_016857543.1	P23246-1A0A384N5Z8
SFPQ	NR_136702.2 link	n.2083-2488G>A	intron_variant	Intron 9 of 11

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SFPQ	ENST00000468598.5 link	n.122G>A	non_coding_transcript_exon_variant	Exon 1 of 3	1
SFPQ	ENST00000460428.5 link	n.241-2488G>A	intron_variant	Intron 3 of 5	2	ENSP00000425071.1	H0Y9U2
SFPQ	ENST00000470472.5 link	n.649-2488G>A	intron_variant	Intron 6 of 8	5	ENSP00000424440.1	H0Y9K7

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35301

AN:

151954

Hom.:

8799

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.0346

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0224

Gnomad OTH

AF:

0.202

GnomAD4 exome

AF:

0.0452

AC:

40535

AN:

897412

Hom.:

7456

Cov.:

AF XY:

0.0430

AC XY:

17826

AN XY:

414494

show subpopulations

African (AFR)

AF:

0.602

AC:

11287

AN:

18734

American (AMR)

AF:

0.340

AC:

978

AN:

2880

Ashkenazi Jewish (ASJ)

AF:

0.0337

AC:

314

AN:

9310

East Asian (EAS)

AF:

0.695

AC:

9045

AN:

13018

South Asian (SAS)

AF:

0.130

AC:

2217

AN:

17010

European-Finnish (FIN)

AF:

0.0994

AC:

AN:

322

Middle Eastern (MID)

AF:

0.0537

AC:

108

AN:

2012

European-Non Finnish (NFE)

AF:

0.0165

AC:

13207

AN:

801402

Other (OTH)

AF:

0.102

AC:

3347

AN:

32724

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

1180

2360

3541

4721

5901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1008

2016

3024

4032

5040

<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:

0.233

AC:

35407

AN:

152072

Hom.:

8834

Cov.:

AF XY:

0.238

AC XY:

17689

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.564

AC:

23359

AN:

41436

American (AMR)

AF:

0.301

AC:

4603

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0346

AC:

120

AN:

3470

East Asian (EAS)

AF:

0.664

AC:

3431

AN:

5166

South Asian (SAS)

AF:

0.141

AC:

678

AN:

4816

European-Finnish (FIN)

AF:

0.117

AC:

1237

AN:

10580

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0224

AC:

1522

AN:

68012

Other (OTH)

AF:

0.207

AC:

437

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

889

1779

2668

3558

4447

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.0931

Hom.:

11958

Bravo

AF:

0.266

Asia WGS

AF:

0.410

AC:

1425

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

0.15

Splicing

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