13-41466897-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014059.3(RGCC):c.310G>A(p.Ala104Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014059.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGCC | NM_014059.3 | c.310G>A | p.Ala104Thr | missense_variant | 3/5 | ENST00000379359.4 | |
RGCC | XR_941565.2 | n.736G>A | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGCC | ENST00000379359.4 | c.310G>A | p.Ala104Thr | missense_variant | 3/5 | 1 | NM_014059.3 | P1 | |
RGCC | ENST00000487837.1 | n.141G>A | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249520Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135368
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461514Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727078
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.310G>A (p.A104T) alteration is located in exon 3 (coding exon 3) of the RGCC gene. This alteration results from a G to A substitution at nucleotide position 310, causing the alanine (A) at amino acid position 104 to be replaced by a threonine (T). 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