7-127698952-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_014390.4(SND1):āc.427A>Cā(p.Asn143His) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,611,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014390.4 missense, splice_region
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.427A>C | p.Asn143His | missense_variant, splice_region_variant | 4/24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.427A>C | p.Asn143His | missense_variant, splice_region_variant | 4/17 | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.427A>C | p.Asn143His | missense_variant, splice_region_variant | 4/24 | 1 | NM_014390.4 | ENSP00000346762 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250656Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135420
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1459754Hom.: 0 Cov.: 29 AF XY: 0.00000964 AC XY: 7AN XY: 726360
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.427A>C (p.N143H) alteration is located in exon 4 (coding exon 4) of the SND1 gene. This alteration results from a A to C substitution at nucleotide position 427, causing the asparagine (N) at amino acid position 143 to be replaced by a histidine (H). 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