chr19-5591786-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014649.3(SAFB2):c.2356G>A(p.Gly786Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014649.3 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 |
---|---|---|---|---|---|---|---|
SAFB2 | NM_014649.3 | c.2356G>A | p.Gly786Ser | missense_variant | 17/21 | ENST00000252542.9 | |
SAFB2 | XM_011528449.4 | c.2356G>A | p.Gly786Ser | missense_variant | 17/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAFB2 | ENST00000252542.9 | c.2356G>A | p.Gly786Ser | missense_variant | 17/21 | 1 | NM_014649.3 | P1 | |
SAFB2 | ENST00000589925.1 | n.224G>A | non_coding_transcript_exon_variant | 3/5 | 3 | ||||
SAFB2 | ENST00000590000.1 | n.143G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251368Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135858
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461830Hom.: 0 Cov.: 30 AF XY: 0.0000743 AC XY: 54AN XY: 727216
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 21, 2021 | The c.2356G>A (p.G786S) alteration is located in exon 17 (coding exon 17) of the SAFB2 gene. This alteration results from a G to A substitution at nucleotide position 2356, causing the glycine (G) at amino acid position 786 to be replaced by a serine (S). 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