chr5-94649596-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_032290.4(SLF1):āc.737A>Gā(p.Gln246Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000936 in 1,468,618 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_032290.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.737A>G | p.Gln246Arg | missense_variant, splice_region_variant | 6/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.737A>G | p.Gln246Arg | missense_variant, splice_region_variant | 6/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000466957.1 | c.361-12702A>G | intron_variant, NMD_transcript_variant | 5 | |||||
SLF1 | ENST00000508130.5 | c.*34A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000644 AC: 98AN: 152208Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00168 AC: 226AN: 134766Hom.: 2 AF XY: 0.00205 AC XY: 146AN XY: 71104
GnomAD4 exome AF: 0.000969 AC: 1275AN: 1316292Hom.: 8 Cov.: 30 AF XY: 0.00118 AC XY: 755AN XY: 641958
GnomAD4 genome AF: 0.000656 AC: 100AN: 152326Hom.: 1 Cov.: 32 AF XY: 0.000792 AC XY: 59AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | SLF1: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at