chr4-672506-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007100.4(ATP5ME):c.204A>T(p.Leu68Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,613,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007100.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP5ME | NM_007100.4 | c.204A>T | p.Leu68Phe | missense_variant | 4/4 | ENST00000304312.5 | |
ATP5ME | NR_033743.2 | n.178A>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP5ME | ENST00000304312.5 | c.204A>T | p.Leu68Phe | missense_variant | 4/4 | 1 | NM_007100.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251028Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135834
GnomAD4 exome AF: 0.000131 AC: 192AN: 1461790Hom.: 0 Cov.: 32 AF XY: 0.000132 AC XY: 96AN XY: 727198
GnomAD4 genome AF: 0.000138 AC: 21AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.204A>T (p.L68F) alteration is located in exon 4 (coding exon 4) of the ATP5I gene. This alteration results from a A to T substitution at nucleotide position 204, causing the leucine (L) at amino acid position 68 to be replaced by a phenylalanine (F). 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