rs10158985
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014698.3(TMEM63A):c.747-58G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,519,338 control chromosomes in the GnomAD database, including 34,298 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 2494 hom., cov: 30)
Exomes 𝑓: 0.21 ( 31804 hom. )
Consequence
TMEM63A
NM_014698.3 intron
NM_014698.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.04
Genes affected
TMEM63A (HGNC:29118): (transmembrane protein 63A) Enables mechanosensitive ion channel activity. Predicted to be involved in cation transmembrane transport. Located in centriolar satellite and lysosomal membrane. Implicated in hypomyelinating leukodystrophy. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM63A | NM_014698.3 | c.747-58G>T | intron_variant | ENST00000366835.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM63A | ENST00000366835.8 | c.747-58G>T | intron_variant | 1 | NM_014698.3 | P1 | |||
TMEM63A | ENST00000537914.5 | c.-232-58G>T | intron_variant | 1 | |||||
TMEM63A | ENST00000474478.5 | n.2456G>T | non_coding_transcript_exon_variant | 2/4 | 2 | ||||
TMEM63A | ENST00000483779.1 | n.515-58G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.167 AC: 25324AN: 151644Hom.: 2496 Cov.: 30
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GnomAD4 exome AF: 0.210 AC: 287107AN: 1367576Hom.: 31804 Cov.: 22 AF XY: 0.208 AC XY: 141720AN XY: 681122
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GnomAD4 genome ? AF: 0.167 AC: 25307AN: 151762Hom.: 2494 Cov.: 30 AF XY: 0.164 AC XY: 12140AN XY: 74132
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at