chr1-225847179-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_014698.3(TMEM63A):c.2285C>T(p.Ser762Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S762S) has been classified as Likely benign.
Frequency
Consequence
NM_014698.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM63A | NM_014698.3 | c.2285C>T | p.Ser762Leu | missense_variant | 24/25 | ENST00000366835.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM63A | ENST00000366835.8 | c.2285C>T | p.Ser762Leu | missense_variant | 24/25 | 1 | NM_014698.3 | P1 | |
TMEM63A | ENST00000482753.1 | n.365C>T | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
TMEM63A | ENST00000496025.1 | n.287C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250034Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135498
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1460994Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726822
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74380
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.2285C>T (p.S762L) alteration is located in exon 24 (coding exon 22) of the TMEM63A gene. This alteration results from a C to T substitution at nucleotide position 2285, causing the serine (S) at amino acid position 762 to be replaced by a leucine (L). 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