chr5-94651835-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032290.4(SLF1):āc.872A>Gā(p.Tyr291Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000795 in 1,257,868 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_032290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.872A>G | p.Tyr291Cys | missense_variant | 7/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.872A>G | p.Tyr291Cys | missense_variant | 7/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000466957.1 | c.361-10463A>G | intron_variant, NMD_transcript_variant | 5 | |||||
SLF1 | ENST00000508130.5 | c.*169A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.95e-7 AC: 1AN: 1257868Hom.: 0 Cov.: 22 AF XY: 0.00000161 AC XY: 1AN XY: 620896
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.872A>G (p.Y291C) alteration is located in exon 7 (coding exon 6) of the SLF1 gene. This alteration results from a A to G substitution at nucleotide position 872, causing the tyrosine (Y) at amino acid position 291 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at