chr19-5661780-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001201338.2(SAFB):c.2125G>A(p.Ala709Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000705 in 1,559,344 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001201338.2 missense
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 |
---|---|---|---|---|---|---|---|
SAFB | NM_001201338.2 | c.2125G>A | p.Ala709Thr | missense_variant | 15/21 | ENST00000588852.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAFB | ENST00000588852.2 | c.2125G>A | p.Ala709Thr | missense_variant | 15/21 | 1 | NM_001201338.2 | P5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000125 AC: 2AN: 160314Hom.: 0 AF XY: 0.0000114 AC XY: 1AN XY: 87624
GnomAD4 exome AF: 0.00000711 AC: 10AN: 1407118Hom.: 0 Cov.: 32 AF XY: 0.00000863 AC XY: 6AN XY: 695246
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.2125G>A (p.A709T) alteration is located in exon 15 (coding exon 15) of the SAFB gene. This alteration results from a G to A substitution at nucleotide position 2125, causing the alanine (A) at amino acid position 709 to be replaced by a threonine (T). 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