7-141742169-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_003143.3(SSBP1):c.25G>A(p.Val9Ile) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000645 in 1,596,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_003143.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152052Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251120Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135756
GnomAD4 exome AF: 0.0000685 AC: 99AN: 1444622Hom.: 0 Cov.: 29 AF XY: 0.0000739 AC XY: 53AN XY: 716826
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152052Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74260
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.25G>A (p.V9I) alteration is located in exon 3 (coding exon 2) of the SSBP1 gene. This alteration results from a G to A substitution at nucleotide position 25, causing the valine (V) at amino acid position 9 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
SSBP1: PM2, BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at