chr5-94651741-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032290.4(SLF1):āc.778A>Gā(p.Ile260Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,523,764 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_032290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.778A>G | p.Ile260Val | missense_variant | 7/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.778A>G | p.Ile260Val | missense_variant | 7/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000466957.1 | c.361-10557A>G | intron_variant, NMD_transcript_variant | 5 | |||||
SLF1 | ENST00000508130.5 | c.*75A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000225 AC: 3AN: 133084Hom.: 0 AF XY: 0.0000424 AC XY: 3AN XY: 70762
GnomAD4 exome AF: 0.0000190 AC: 26AN: 1371566Hom.: 1 Cov.: 29 AF XY: 0.0000192 AC XY: 13AN XY: 675904
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74364
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at