7-93131311-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152703.5(SAMD9L):c.4661G>C(p.Gly1554Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,784 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 Uncertain significance (★).
Frequency
Consequence
NM_152703.5 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 |
---|---|---|---|---|---|---|---|
SAMD9L | NM_152703.5 | c.4661G>C | p.Gly1554Ala | missense_variant | 5/5 | ENST00000318238.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAMD9L | ENST00000318238.9 | c.4661G>C | p.Gly1554Ala | missense_variant | 5/5 | 1 | NM_152703.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250198Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135220
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460784Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726702
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
SAMD9L-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 25, 2023 | The SAMD9L c.4661G>C variant is predicted to result in the amino acid substitution p.Gly1554Ala. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-92760624-C-G). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at