dbSNP rs1062753: SEPTIN3:c.*2051G>A (chr22-41996807-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 ENST00000396425.8(SEPTIN3):c.*2051G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,572,938 control chromosomes in the GnomAD database, including 68,377 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 0.29 ( 6937 hom., cov: 31)

Exomes 𝑓: 0.29 ( 61440 hom. )

Consequence

SEPTIN3
ENST00000396425.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.222

Publications

40 publications found

Variant links:

Genes affected

SEPTIN3 (HGNC:10750): (septin 3) This gene belongs to the septin family of GTPases. Members of this family are required for cytokinesis. Expression is upregulated by retinoic acid in a human teratocarcinoma cell line. The specific function of this gene has not been determined. Alternative splicing of this gene results in several transcript variants encoding different isoforms. [provided by RefSeq, May 2018]

SEPTIN3 links:

ENSG00000301540 (HGNC:):

ENSG00000301540 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000396425.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SEPTIN3	NM_001363845.2	MANE Select	c.2506-95G>A	intron	N/A	NP_001350774.1
SEPTIN3	NM_001389668.1		c.*2051G>A	3_prime_UTR	Exon 11 of 11	NP_001376597.1
SEPTIN3	NM_001389671.1		c.*2051G>A	3_prime_UTR	Exon 10 of 10	NP_001376600.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SEPTIN3	ENST00000396425.8	TSL:1	c.*2051G>A	3_prime_UTR	Exon 10 of 10	ENSP00000379703.3
SEPTIN3	ENST00000644076.2	MANE Select	c.2506-95G>A	intron	N/A	ENSP00000494051.1
SEPTIN3	ENST00000396426.7	TSL:1	c.1012-95G>A	intron	N/A	ENSP00000379704.3

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44272

AN:

151938

Hom.:

6930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.367

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.0521

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.298

GnomAD4 exome

AF:

0.286

AC:

406971

AN:

1420882

Hom.:

61440

Cov.:

AF XY:

0.284

AC XY:

199492

AN XY:

702120

show subpopulations

African (AFR)

AF:

0.320

AC:

10445

AN:

32616

American (AMR)

AF:

0.448

AC:

18219

AN:

40632

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

8484

AN:

23270

East Asian (EAS)

AF:

0.0421

AC:

1649

AN:

39192

South Asian (SAS)

AF:

0.245

AC:

19784

AN:

80602

European-Finnish (FIN)

AF:

0.137

AC:

7005

AN:

51266

Middle Eastern (MID)

AF:

0.273

AC:

1526

AN:

5582

European-Non Finnish (NFE)

AF:

0.297

AC:

323210

AN:

1089132

Other (OTH)

AF:

0.284

AC:

16649

AN:

58590

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

15550

31099

46649

62198

77748

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10852

21704

32556

43408

54260

<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:

0.291

AC:

44301

AN:

152056

Hom.:

6937

Cov.:

AF XY:

0.282

AC XY:

20934

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.322

AC:

13353

AN:

41422

American (AMR)

AF:

0.367

AC:

5604

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

1302

AN:

3468

East Asian (EAS)

AF:

0.0511

AC:

265

AN:

5186

South Asian (SAS)

AF:

0.243

AC:

1175

AN:

4826

European-Finnish (FIN)

AF:

0.126

AC:

1339

AN:

10612

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.298

AC:

20272

AN:

67948

Other (OTH)

AF:

0.294

AC:

621

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1521

3042

4562

6083

7604

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.297

Hom.:

30982

Bravo

AF:

0.312

Asia WGS

AF:

0.179

AC:

624

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.0

(source)

DANN

Benign

0.67

PhyloP100

-0.22

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