7-127686609-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014390.4(SND1):c.79-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,613,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014390.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.79-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000354725.8 | NP_055205.2 | |||
SND1 | XM_017011987.3 | c.79-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.79-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014390.4 | ENSP00000346762 | P1 | |||
SND1 | ENST00000461056.5 | n.222-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 4 | ||||||
SND1 | ENST00000463020.1 | n.259-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 | ||||||
SND1 | ENST00000468621.5 | n.94-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 41AN: 250732Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135458
GnomAD4 exome AF: 0.0000849 AC: 124AN: 1461106Hom.: 0 Cov.: 30 AF XY: 0.0000743 AC XY: 54AN XY: 726720
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74312
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 11, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at