rs1062753

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.222
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SEPTIN3NM_001363845.2 linkuse as main transcriptc.2506-95G>A intron_variant ENST00000644076.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SEPTIN3ENST00000644076.2 linkuse as main transcriptc.2506-95G>A intron_variant NM_001363845.2

Frequencies

GnomAD3 genomes
AF:
0.291
AC:
44272
AN:
151938
Hom.:
6930
Cov.:
31
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.:
36
AF XY:
0.284
AC XY:
199492
AN XY:
702120
show subpopulations
Gnomad4 AFR exome
AF:
0.320
Gnomad4 AMR exome
AF:
0.448
Gnomad4 ASJ exome
AF:
0.365
Gnomad4 EAS exome
AF:
0.0421
Gnomad4 SAS exome
AF:
0.245
Gnomad4 FIN exome
AF:
0.137
Gnomad4 NFE exome
AF:
0.297
Gnomad4 OTH exome
AF:
0.284
GnomAD4 genome
AF:
0.291
AC:
44301
AN:
152056
Hom.:
6937
Cov.:
31
AF XY:
0.282
AC XY:
20934
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.322
Gnomad4 AMR
AF:
0.367
Gnomad4 ASJ
AF:
0.375
Gnomad4 EAS
AF:
0.0511
Gnomad4 SAS
AF:
0.243
Gnomad4 FIN
AF:
0.126
Gnomad4 NFE
AF:
0.298
Gnomad4 OTH
AF:
0.294
Alfa
AF:
0.297
Hom.:
14183
Bravo
AF:
0.312
Asia WGS
AF:
0.179
AC:
624
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.0
DANN
Benign
0.67

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1062753; hg19: chr22-42392811; COSMIC: COSV52173473; COSMIC: COSV52173473; API