5-146339182-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001414499.1(LOC127814297):c.2903C>T(p.Ser968Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S968S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001414499.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000275740 | ENST00000506502.2 | c.3026C>T | p.Ser1009Phe | missense_variant | Exon 20 of 20 | 5 | ENSP00000475384.1 | |||
POU4F3 | ENST00000646991.2 | c.70C>T | p.Leu24Leu | synonymous_variant | Exon 1 of 2 | NM_002700.3 | ENSP00000495718.1 | |||
ENSG00000250025 | ENST00000515598.1 | n.404-31906G>A | intron_variant | Intron 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000919 AC: 14AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251464Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135906
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727246
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74382
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at