chr1-225847146-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014698.3(TMEM63A):c.2318A>G(p.Gln773Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000886 in 1,613,410 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_014698.3 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 |
---|---|---|---|---|---|---|---|
TMEM63A | NM_014698.3 | c.2318A>G | p.Gln773Arg | missense_variant | 24/25 | ENST00000366835.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM63A | ENST00000366835.8 | c.2318A>G | p.Gln773Arg | missense_variant | 24/25 | 1 | NM_014698.3 | P1 | |
TMEM63A | ENST00000482753.1 | n.398A>G | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
TMEM63A | ENST00000496025.1 | n.320A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250722Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135698
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461148Hom.: 0 Cov.: 31 AF XY: 0.0000922 AC XY: 67AN XY: 726898
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74398
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.2318A>G (p.Q773R) alteration is located in exon 24 (coding exon 22) of the TMEM63A gene. This alteration results from a A to G substitution at nucleotide position 2318, causing the glutamine (Q) at amino acid position 773 to be replaced by an arginine (R). 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