1-54405990-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_145716.4(SSBP3):c.19G>A(p.Gly7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000673 in 1,486,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145716.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSBP3 | NM_145716.4 | c.19G>A | p.Gly7Ser | missense_variant | Exon 1 of 18 | NP_663768.1 | ||
SSBP3 | NM_001394360.1 | c.19G>A | p.Gly7Ser | missense_variant | Exon 1 of 17 | NP_001381289.1 | ||
SSBP3 | NM_018070.5 | c.19G>A | p.Gly7Ser | missense_variant | Exon 1 of 17 | NP_060540.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSBP3 | ENST00000610401.6 | c.19G>A | p.Gly7Ser | missense_variant | Exon 1 of 18 | 5 | ENSP00000479674.2 | |||
SSBP3 | ENST00000357475.9 | c.19G>A | p.Gly7Ser | missense_variant | Exon 1 of 17 | 1 | ENSP00000350067.4 | |||
SSBP3 | ENST00000371319.8 | c.19G>A | p.Gly7Ser | missense_variant | Exon 1 of 17 | 2 | ENSP00000360370.3 | |||
SSBP3 | ENST00000525990.1 | c.-274-1060G>A | intron_variant | Intron 1 of 8 | 2 | ENSP00000431654.1 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150286Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000734 AC: 1AN: 136282Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 76372
GnomAD4 exome AF: 0.00000673 AC: 9AN: 1336474Hom.: 0 Cov.: 31 AF XY: 0.00000302 AC XY: 2AN XY: 662286
GnomAD4 genome AF: 0.00000665 AC: 1AN: 150286Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 73352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.19G>A (p.G7S) alteration is located in exon 1 (coding exon 1) of the SSBP3 gene. This alteration results from a G to A substitution at nucleotide position 19, causing the glycine (G) at amino acid position 7 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