22-19720124-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_002688.6(SEPTIN5):c.248G>A(p.Ser83Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 1,613,008 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 Likely benign (★).
Frequency
Consequence
NM_002688.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN5 | NM_002688.6 | c.248G>A | p.Ser83Asn | missense_variant | 5/12 | ENST00000455784.7 | |
SEPT5-GP1BB | NR_037611.1 | n.1793G>A | non_coding_transcript_exon_variant | 4/12 | |||
SEPTIN5 | NM_001009939.3 | c.275G>A | p.Ser92Asn | missense_variant | 4/11 | ||
SEPT5-GP1BB | NR_037612.1 | n.297G>A | non_coding_transcript_exon_variant | 4/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN5 | ENST00000455784.7 | c.248G>A | p.Ser83Asn | missense_variant | 5/12 | 1 | NM_002688.6 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 250100Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135646
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1460754Hom.: 0 Cov.: 32 AF XY: 0.0000908 AC XY: 66AN XY: 726664
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74382
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at