chr7-127701242-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014390.4(SND1):āc.508T>Gā(p.Ser170Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,613,918 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.508T>G | p.Ser170Ala | missense_variant | 5/24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.508T>G | p.Ser170Ala | missense_variant | 5/17 | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.508T>G | p.Ser170Ala | missense_variant | 5/24 | 1 | NM_014390.4 | ENSP00000346762 | P1 | |
SND1 | ENST00000483503.5 | n.403T>G | non_coding_transcript_exon_variant | 4/6 | 5 | |||||
SND1 | ENST00000492772.1 | n.315T>G | non_coding_transcript_exon_variant | 4/6 | 4 | |||||
SND1 | ENST00000468621.5 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251328Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135812
GnomAD4 exome AF: 0.000163 AC: 238AN: 1461806Hom.: 2 Cov.: 31 AF XY: 0.000169 AC XY: 123AN XY: 727198
GnomAD4 genome AF: 0.000118 AC: 18AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2022 | The c.508T>G (p.S170A) alteration is located in exon 5 (coding exon 5) of the SND1 gene. This alteration results from a T to G substitution at nucleotide position 508, causing the serine (S) at amino acid position 170 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