chr14-77720751-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_012245.3(SNW1):āc.1208A>Gā(p.Asn403Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,918 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_012245.3 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 | UniProt |
---|---|---|---|---|---|---|---|
SNW1 | NM_012245.3 | c.1208A>G | p.Asn403Ser | missense_variant | 12/14 | ENST00000261531.12 | |
SNW1 | NM_001318844.2 | c.1208A>G | p.Asn403Ser | missense_variant | 12/13 | ||
SNW1 | XM_047431112.1 | c.1111A>G | p.Met371Val | missense_variant | 11/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNW1 | ENST00000261531.12 | c.1208A>G | p.Asn403Ser | missense_variant | 12/14 | 1 | NM_012245.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251398Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135870
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461622Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 727110
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1208A>G (p.N403S) alteration is located in exon 12 (coding exon 12) of the SNW1 gene. This alteration results from a A to G substitution at nucleotide position 1208, causing the asparagine (N) at amino acid position 403 to be replaced by a serine (S). 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