19-5661645-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001201338.2(SAFB):āc.1990A>Cā(p.Met664Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,612,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001201338.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAFB | NM_001201338.2 | c.1990A>C | p.Met664Leu | missense_variant | 15/21 | ENST00000588852.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAFB | ENST00000588852.2 | c.1990A>C | p.Met664Leu | missense_variant | 15/21 | 1 | NM_001201338.2 | P5 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000135 AC: 33AN: 244004Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 133382
GnomAD4 exome AF: 0.0000555 AC: 81AN: 1459958Hom.: 0 Cov.: 32 AF XY: 0.0000496 AC XY: 36AN XY: 726350
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.1990A>C (p.M664L) alteration is located in exon 15 (coding exon 15) of the SAFB gene. This alteration results from a A to C substitution at nucleotide position 1990, causing the methionine (M) at amino acid position 664 to be replaced by a leucine (L). 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