dbSNP rs10401969: SUGP1:c.1243+80A>G (chr19-19296909-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_172231.4(SUGP1):c.1243+80A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0812 in 1,198,724 control chromosomes in the GnomAD database, including 4,332 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 0.10 ( 931 hom., cov: 32)

Exomes 𝑓: 0.078 ( 3401 hom. )

Consequence

SUGP1
NM_172231.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

260 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

new If you want to explore the variant's impact on the transcript NM_172231.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172231.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGP1	NM_172231.4	MANE Select	c.1243+80A>G		intron	N/A	NP_757386.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SUGP1	ENST00000247001.10	TSL:1 MANE Select	c.1243+80A>G	intron	N/A	ENSP00000247001.3	Q8IWZ8-1
SUGP1	ENST00000588731.6	TSL:1	n.*770+80A>G	intron	N/A	ENSP00000465413.2	Q8IWZ8-2
SUGP1	ENST00000589144.5	TSL:1	n.*506+80A>G	intron	N/A	ENSP00000466402.3	K7EM86

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15248

AN:

152094

Hom.:

916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.0717

Gnomad ASJ

AF:

0.0475

Gnomad EAS

AF:

0.0993

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.0579

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0738

Gnomad OTH

AF:

0.0823

GnomAD4 exome

AF:

0.0784

AC:

82017

AN:

1046512

Hom.:

3401

AF XY:

0.0784

AC XY:

40447

AN XY:

515740

show subpopulations

African (AFR)

AF:

0.170

AC:

4089

AN:

23992

American (AMR)

AF:

0.0531

AC:

1129

AN:

21264

Ashkenazi Jewish (ASJ)

AF:

0.0543

AC:

935

AN:

17210

East Asian (EAS)

AF:

0.101

AC:

3450

AN:

34266

South Asian (SAS)

AF:

0.0976

AC:

5586

AN:

57254

European-Finnish (FIN)

AF:

0.0625

AC:

2213

AN:

35394

Middle Eastern (MID)

AF:

0.0529

AC:

165

AN:

3120

European-Non Finnish (NFE)

AF:

0.0753

AC:

60888

AN:

808508

Other (OTH)

AF:

0.0783

AC:

3562

AN:

45504

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

3765

7530

11296

15061

18826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2290

4580

6870

9160

11450

<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:

0.101

AC:

15301

AN:

152212

Hom.:

931

Cov.:

AF XY:

0.0998

AC XY:

7428

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.171

AC:

7087

AN:

41524

American (AMR)

AF:

0.0716

AC:

1094

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0475

AC:

165

AN:

3472

East Asian (EAS)

AF:

0.0991

AC:

513

AN:

5174

South Asian (SAS)

AF:

0.102

AC:

494

AN:

4830

European-Finnish (FIN)

AF:

0.0579

AC:

615

AN:

10614

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0738

AC:

5018

AN:

67998

Other (OTH)

AF:

0.0900

AC:

190

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

700

1400

2100

2800

3500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<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:

0.0829

Hom.:

2595

Bravo

AF:

0.105

Asia WGS

AF:

0.140

AC:

487

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.2

(source)

DANN

Benign

0.73

PhyloP100

0.24

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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