20-35954196-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_033630.3(SCAND1):āc.89C>Gā(p.Ala30Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A30V) has been classified as Uncertain significance.
Frequency
Consequence
NM_033630.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAND1 | NM_033630.3 | c.89C>G | p.Ala30Gly | missense_variant | 2/2 | ENST00000305978.7 | |
SCAND1 | NM_001385710.1 | c.89C>G | p.Ala30Gly | missense_variant | 3/3 | ||
SCAND1 | NM_016558.4 | c.89C>G | p.Ala30Gly | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAND1 | ENST00000305978.7 | c.89C>G | p.Ala30Gly | missense_variant | 2/2 | 1 | NM_033630.3 | P1 | |
SCAND1 | ENST00000373991.3 | c.89C>G | p.Ala30Gly | missense_variant | 3/3 | 1 | P1 | ||
SCAND1 | ENST00000615116.1 | c.89C>G | p.Ala30Gly | missense_variant | 3/3 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459702Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726256
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | 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