chr11-106986124-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000855.3(GUCY1A2):c.311C>T(p.Thr104Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 1,434,398 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_000855.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY1A2 | NM_000855.3 | c.311C>T | p.Thr104Met | missense_variant | 2/8 | ENST00000526355.7 | |
GUCY1A2 | NM_001256424.2 | c.311C>T | p.Thr104Met | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY1A2 | ENST00000526355.7 | c.311C>T | p.Thr104Met | missense_variant | 2/8 | 1 | NM_000855.3 | P1 | |
GUCY1A2 | ENST00000282249.6 | c.311C>T | p.Thr104Met | missense_variant | 2/9 | 1 | |||
GUCY1A2 | ENST00000347596.2 | c.311C>T | p.Thr104Met | missense_variant | 2/9 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250328Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135360
GnomAD4 exome AF: 0.0000101 AC: 13AN: 1282386Hom.: 0 Cov.: 20 AF XY: 0.00000463 AC XY: 3AN XY: 648156
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 152012Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.311C>T (p.T104M) alteration is located in exon 2 (coding exon 2) of the GUCY1A2 gene. This alteration results from a C to T substitution at nucleotide position 311, causing the threonine (T) at amino acid position 104 to be replaced by a methionine (M). 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