chr5-94630530-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032290.4(SLF1):āc.218T>Cā(p.Ile73Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000214 in 1,399,244 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0000021 ( 0 hom. )
Consequence
SLF1
NM_032290.4 missense
NM_032290.4 missense
Scores
5
8
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.49
Genes affected
SLF1 (HGNC:25408): (SMC5-SMC6 complex localization factor 1) Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in nucleoplasm and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.218T>C | p.Ile73Thr | missense_variant | 4/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.218T>C | p.Ile73Thr | missense_variant | 4/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000504099.5 | c.218T>C | p.Ile73Thr | missense_variant | 5/5 | 4 | |||
SLF1 | ENST00000508130.5 | c.218T>C | p.Ile73Thr | missense_variant, NMD_transcript_variant | 4/8 | 2 | |||
SLF1 | ENST00000466957.1 | c.149T>C | p.Ile50Thr | missense_variant, NMD_transcript_variant | 3/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399244Hom.: 0 Cov.: 30 AF XY: 0.00000290 AC XY: 2AN XY: 690116
GnomAD4 exome
AF:
AC:
3
AN:
1399244
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
690116
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;D
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Loss of stability (P = 0.0137);Loss of stability (P = 0.0137);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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
No publications associated with this variant yet.