chr1-54257165-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_145716.4(SSBP3):c.469G>A(p.Ala157Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00033 in 1,601,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSBP3 | NM_145716.4 | c.469G>A | p.Ala157Thr | missense_variant | Exon 7 of 18 | NP_663768.1 | ||
SSBP3 | NM_001394360.1 | c.388G>A | p.Ala130Thr | missense_variant | Exon 6 of 17 | NP_001381289.1 | ||
SSBP3 | NM_001009955.4 | c.388G>A | p.Ala130Thr | missense_variant | Exon 6 of 17 | NP_001009955.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSBP3 | ENST00000610401.6 | c.469G>A | p.Ala157Thr | missense_variant | Exon 7 of 18 | 5 | ENSP00000479674.2 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000370 AC: 88AN: 238106Hom.: 0 AF XY: 0.000317 AC XY: 41AN XY: 129184
GnomAD4 exome AF: 0.000329 AC: 477AN: 1449686Hom.: 0 Cov.: 31 AF XY: 0.000293 AC XY: 211AN XY: 721010
GnomAD4 genome AF: 0.000335 AC: 51AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.469G>A (p.A157T) alteration is located in exon 7 (coding exon 7) of the SSBP3 gene. This alteration results from a G to A substitution at nucleotide position 469, causing the alanine (A) at amino acid position 157 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