chr11-107017857-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000855.3(GUCY1A2):c.199G>T(p.Ala67Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,251,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000855.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY1A2 | NM_000855.3 | c.199G>T | p.Ala67Ser | missense_variant | 1/8 | ENST00000526355.7 | |
GUCY1A2 | NM_001256424.2 | c.199G>T | p.Ala67Ser | missense_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY1A2 | ENST00000526355.7 | c.199G>T | p.Ala67Ser | missense_variant | 1/8 | 1 | NM_000855.3 | P1 | |
GUCY1A2 | ENST00000282249.6 | c.199G>T | p.Ala67Ser | missense_variant | 1/9 | 1 | |||
GUCY1A2 | ENST00000347596.2 | c.199G>T | p.Ala67Ser | missense_variant | 1/9 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000462 AC: 7AN: 151552Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000216 AC: 238AN: 1100206Hom.: 0 Cov.: 29 AF XY: 0.000215 AC XY: 113AN XY: 524528
GnomAD4 genome ? AF: 0.0000462 AC: 7AN: 151660Hom.: 0 Cov.: 33 AF XY: 0.0000405 AC XY: 3AN XY: 74106
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.199G>T (p.A67S) alteration is located in exon 1 (coding exon 1) of the GUCY1A2 gene. This alteration results from a G to T substitution at nucleotide position 199, causing the alanine (A) at amino acid position 67 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