chr1-225850026-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014698.3(TMEM63A):c.1957G>A(p.Val653Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000152 in 1,614,158 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_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.1957G>A | p.Val653Ile | missense_variant | 21/25 | ENST00000366835.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM63A | ENST00000366835.8 | c.1957G>A | p.Val653Ile | missense_variant | 21/25 | 1 | NM_014698.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251472Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135918
GnomAD4 exome AF: 0.000150 AC: 219AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.000144 AC XY: 105AN XY: 727246
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74454
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.1957G>A (p.V653I) alteration is located in exon 21 (coding exon 19) of the TMEM63A gene. This alteration results from a G to A substitution at nucleotide position 1957, causing the valine (V) at amino acid position 653 to be replaced by an isoleucine (I). 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