1-9730639-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001009566.3(CLSTN1):c.2815G>A(p.Gly939Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000807 in 1,610,446 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_001009566.3 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 |
---|---|---|---|---|---|---|---|---|
CLSTN1 | NM_001009566.3 | c.2815G>A | p.Gly939Ser | missense_variant | Exon 19 of 19 | ENST00000377298.9 | NP_001009566.1 | |
CLSTN1 | NM_014944.4 | c.2785G>A | p.Gly929Ser | missense_variant | Exon 18 of 18 | NP_055759.3 | ||
CLSTN1 | NM_001302883.1 | c.2758G>A | p.Gly920Ser | missense_variant | Exon 18 of 18 | NP_001289812.1 | ||
CLSTN1 | XM_047449470.1 | c.2728G>A | p.Gly910Ser | missense_variant | Exon 17 of 17 | XP_047305426.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000806 AC: 20AN: 248124Hom.: 0 AF XY: 0.0000520 AC XY: 7AN XY: 134504
GnomAD4 exome AF: 0.0000850 AC: 124AN: 1458396Hom.: 0 Cov.: 31 AF XY: 0.0000785 AC XY: 57AN XY: 725694
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2815G>A (p.G939S) alteration is located in exon 19 (coding exon 19) of the CLSTN1 gene. This alteration results from a G to A substitution at nucleotide position 2815, causing the glycine (G) at amino acid position 939 to be replaced by a serine (S). 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