7-127701188-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014390.4(SND1):āc.454T>Gā(p.Cys152Gly) 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 1,461,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014390.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.454T>G | p.Cys152Gly | missense_variant | 5/24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.454T>G | p.Cys152Gly | missense_variant | 5/17 | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.454T>G | p.Cys152Gly | missense_variant | 5/24 | 1 | NM_014390.4 | ENSP00000346762 | P1 | |
SND1 | ENST00000468621.5 | n.469T>G | non_coding_transcript_exon_variant | 5/5 | 4 | |||||
SND1 | ENST00000483503.5 | n.349T>G | non_coding_transcript_exon_variant | 4/6 | 5 | |||||
SND1 | ENST00000492772.1 | n.261T>G | non_coding_transcript_exon_variant | 4/6 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251232Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135758
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461782Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727182
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.454T>G (p.C152G) alteration is located in exon 5 (coding exon 5) of the SND1 gene. This alteration results from a T to G substitution at nucleotide position 454, causing the cysteine (C) at amino acid position 152 to be replaced by a glycine (G). 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