rs773717301
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_032740.4(SFT2D3):c.179C>A(p.Ser60*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000603 in 1,327,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Consequence
SFT2D3
NM_032740.4 stop_gained
NM_032740.4 stop_gained
Scores
2
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.26
Publications
1 publications found
Genes affected
SFT2D3 (HGNC:28767): (SFT2 domain containing 3) Predicted to be involved in protein transport and vesicle-mediated transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
WDR33 (HGNC:25651): (WD repeat domain 33) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This gene is highly expressed in testis and the protein is localized to the nucleus. This gene may play important roles in the mechanisms of cytodifferentiation and/or DNA recombination. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFT2D3 | NM_032740.4 | c.179C>A | p.Ser60* | stop_gained | Exon 1 of 1 | ENST00000310981.6 | NP_116129.3 | |
WDR33 | NM_018383.5 | c.*4616G>T | 3_prime_UTR_variant | Exon 22 of 22 | ENST00000322313.9 | NP_060853.3 | ||
WDR33 | XM_011511436.2 | c.*4616G>T | 3_prime_UTR_variant | Exon 22 of 22 | XP_011509738.1 | |||
WDR33 | XM_005263697.4 | c.*4786G>T | 3_prime_UTR_variant | Exon 21 of 21 | XP_005263754.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFT2D3 | ENST00000310981.6 | c.179C>A | p.Ser60* | stop_gained | Exon 1 of 1 | 6 | NM_032740.4 | ENSP00000310803.3 | ||
WDR33 | ENST00000322313.9 | c.*4616G>T | 3_prime_UTR_variant | Exon 22 of 22 | 1 | NM_018383.5 | ENSP00000325377.3 | |||
ENSG00000293688 | ENST00000718293.1 | n.-247G>T | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151164Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
151164
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00 AC: 0AN: 13670 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
13670
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000425 AC: 5AN: 1175862Hom.: 0 Cov.: 31 AF XY: 0.00000349 AC XY: 2AN XY: 573148 show subpopulations
GnomAD4 exome
AF:
AC:
5
AN:
1175862
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
573148
show subpopulations
African (AFR)
AF:
AC:
4
AN:
23430
American (AMR)
AF:
AC:
0
AN:
10366
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
15822
East Asian (EAS)
AF:
AC:
0
AN:
25826
South Asian (SAS)
AF:
AC:
1
AN:
46936
European-Finnish (FIN)
AF:
AC:
0
AN:
27288
Middle Eastern (MID)
AF:
AC:
0
AN:
3198
European-Non Finnish (NFE)
AF:
AC:
0
AN:
975850
Other (OTH)
AF:
AC:
0
AN:
47146
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.445
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151272Hom.: 0 Cov.: 33 AF XY: 0.0000271 AC XY: 2AN XY: 73926 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
151272
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
73926
show subpopulations
African (AFR)
AF:
AC:
3
AN:
41420
American (AMR)
AF:
AC:
0
AN:
15184
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3462
East Asian (EAS)
AF:
AC:
0
AN:
5156
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10220
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67708
Other (OTH)
AF:
AC:
0
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.608
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
PhyloP100
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.