chr22-19714623-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002688.6(SEPTIN5):c.35C>T(p.Ala12Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000398 in 1,505,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A12A) has been classified as Benign.
Frequency
Consequence
NM_002688.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN5 | NM_002688.6 | c.35C>T | p.Ala12Val | missense_variant | 1/12 | ENST00000455784.7 | |
LOC124905079 | XR_007068003.1 | n.99+74G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN5 | ENST00000455784.7 | c.35C>T | p.Ala12Val | missense_variant | 1/12 | 1 | NM_002688.6 | ||
SEPTIN5 | ENST00000406395.5 | c.35C>T | p.Ala12Val | missense_variant | 1/12 | 5 | |||
SEPTIN5 | ENST00000406172.6 | c.35C>T | p.Ala12Val | missense_variant, NMD_transcript_variant | 1/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000667 AC: 1AN: 149844Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000295 AC: 4AN: 1355710Hom.: 0 Cov.: 33 AF XY: 0.00000299 AC XY: 2AN XY: 669030
GnomAD4 genome ? AF: 0.0000133 AC: 2AN: 149956Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2022 | The c.35C>T (p.A12V) alteration is located in exon 1 (coding exon 1) of the SEPT5 gene. This alteration results from a C to T substitution at nucleotide position 35, causing the alanine (A) at amino acid position 12 to be replaced by a valine (V). 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