chr7-127694891-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_014390.4(SND1):c.292A>G(p.Thr98Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000162 in 1,613,846 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 (★). Synonymous variant affecting the same amino acid position (i.e. T98T) has been classified as Likely benign.
Frequency
Consequence
NM_014390.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.292A>G | p.Thr98Ala | missense_variant | 3/24 | ENST00000354725.8 | |
SND1 | XM_017011987.3 | c.292A>G | p.Thr98Ala | missense_variant | 3/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.292A>G | p.Thr98Ala | missense_variant | 3/24 | 1 | NM_014390.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000223 AC: 56AN: 250866Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135572
GnomAD4 exome AF: 0.000170 AC: 249AN: 1461646Hom.: 0 Cov.: 30 AF XY: 0.000160 AC XY: 116AN XY: 727118
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.292A>G (p.T98A) alteration is located in exon 3 (coding exon 3) of the SND1 gene. This alteration results from a A to G substitution at nucleotide position 292, causing the threonine (T) at amino acid position 98 to be replaced by an alanine (A). 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