chr7-127703300-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014390.4(SND1):āc.817A>Gā(p.Ile273Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.817A>G | p.Ile273Val | missense_variant | 7/24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.817A>G | p.Ile273Val | missense_variant | 7/17 | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.817A>G | p.Ile273Val | missense_variant | 7/24 | 1 | NM_014390.4 | ENSP00000346762 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251092Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135672
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727196
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | The c.817A>G (p.I273V) alteration is located in exon 7 (coding exon 7) of the SND1 gene. This alteration results from a A to G substitution at nucleotide position 817, causing the isoleucine (I) at amino acid position 273 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