Genetic Variant SUGP1:c.1781+97C>T (chr19-19277637-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 NM_172231.4(SUGP1):c.1781+97C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 1,473,280 control chromosomes in the GnomAD database, including 3,685 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 0.053 ( 353 hom., cov: 32)

Exomes 𝑓: 0.067 ( 3332 hom. )

Consequence

SUGP1
NM_172231.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.55

Publications

3 publications found

Variant links:

Genes affected

SUGP1 (HGNC:18643): (SURP and G-patch domain containing 1) SF4 is a member of the SURP family of splicing factors.[supplied by OMIM, Sep 2003]

SUGP1 links:

Genome browser will be placed here

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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUGP1	NM_172231.4 link	c.1781+97C>T		intron_variant	Intron 12 of 13	ENST00000247001.10	NP_757386.2	Q8IWZ8-1
SUGP1	XM_047439142.1 link	c.1151+97C>T		intron_variant	Intron 10 of 11		XP_047295098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUGP1	ENST00000247001.10 link	c.1781+97C>T		intron_variant	Intron 12 of 13	1	NM_172231.4	ENSP00000247001.3		Q8IWZ8-1

Frequencies

GnomAD3 genomes

AF:

0.0534

AC:

8129

AN:

152092

Hom.:

354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0123

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0299

Gnomad ASJ

AF:

0.0620

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0522

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0775

Gnomad OTH

AF:

0.0397

GnomAD4 exome

AF:

0.0668

AC:

88215

AN:

1321070

Hom.:

3332

AF XY:

0.0672

AC XY:

43722

AN XY:

650562

show subpopulations

African (AFR)

AF:

0.00933

AC:

287

AN:

30776

American (AMR)

AF:

0.0242

AC:

862

AN:

35680

Ashkenazi Jewish (ASJ)

AF:

0.0665

AC:

1443

AN:

21702

East Asian (EAS)

AF:

0.000319

AC:

AN:

37612

South Asian (SAS)

AF:

0.0650

AC:

4804

AN:

73910

European-Finnish (FIN)

AF:

0.119

AC:

4725

AN:

39762

Middle Eastern (MID)

AF:

0.0459

AC:

214

AN:

4664

European-Non Finnish (NFE)

AF:

0.0708

AC:

72310

AN:

1021574

Other (OTH)

AF:

0.0642

AC:

3558

AN:

55390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3974

7947

11921

15894

19868

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2606

5212

7818

10424

13030

<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:

0.0534

AC:

8123

AN:

152210

Hom.:

353

Cov.:

AF XY:

0.0554

AC XY:

4121

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0122

AC:

508

AN:

41534

American (AMR)

AF:

0.0298

AC:

456

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0620

AC:

215

AN:

3470

East Asian (EAS)

AF:

0.000772

AC:

AN:

5178

South Asian (SAS)

AF:

0.0520

AC:

251

AN:

4828

European-Finnish (FIN)

AF:

0.121

AC:

1288

AN:

10604

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0774

AC:

5265

AN:

67982

Other (OTH)

AF:

0.0388

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

383

767

1150

1534

1917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.0631

Hom.:

515

Bravo

AF:

0.0428

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.099

(source)

DANN

Benign

0.46

PhyloP100

-1.6

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