rs17002342

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018243.4(SEPTIN11):​c.1275-445T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,302 control chromosomes in the GnomAD database, including 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 0.039 ( 377 hom., cov: 33)

Consequence

SEPTIN11
NM_018243.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20
Variant links:
Genes affected
SEPTIN11 (HGNC:25589): (septin 11) SEPT11 belongs to the conserved septin family of filament-forming cytoskeletal GTPases that are involved in a variety of cellular functions including cytokinesis and vesicle trafficking (Hanai et al., 2004 [PubMed 15196925]; Nagata et al., 2004 [PubMed 15485874]).[supplied by OMIM, Jul 2009]

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=-0.78).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SEPTIN11NM_018243.4 linkuse as main transcriptc.1275-445T>A intron_variant ENST00000264893.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SEPTIN11ENST00000264893.11 linkuse as main transcriptc.1275-445T>A intron_variant 1 NM_018243.4 P4Q9NVA2-1

Frequencies

GnomAD3 genomes
AF:
0.0391
AC:
5948
AN:
152184
Hom.:
377
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.136
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0133
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.000564
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.000544
Gnomad OTH
AF:
0.0220
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0391
AC:
5955
AN:
152302
Hom.:
377
Cov.:
33
AF XY:
0.0369
AC XY:
2750
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.136
Gnomad4 AMR
AF:
0.0132
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.000564
Gnomad4 NFE
AF:
0.000544
Gnomad4 OTH
AF:
0.0217
Alfa
AF:
0.0249
Hom.:
28
Bravo
AF:
0.0449
Asia WGS
AF:
0.00635
AC:
22
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
8.4
DANN
Benign
0.76

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: rs17002342; hg19: chr4-77955205; API