7-127694910-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014390.4(SND1):c.311C>T(p.Pro104Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000855 in 1,613,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014390.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.311C>T | p.Pro104Leu | missense_variant | Exon 3 of 24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.311C>T | p.Pro104Leu | missense_variant | Exon 3 of 17 | XP_016867476.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250760Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135502
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461532Hom.: 0 Cov.: 30 AF XY: 0.0000935 AC XY: 68AN XY: 727066
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.311C>T (p.P104L) alteration is located in exon 3 (coding exon 3) of the SND1 gene. This alteration results from a C to T substitution at nucleotide position 311, causing the proline (P) at amino acid position 104 to be replaced by a leucine (L). 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