chr4-673345-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007100.4(ATP5ME):āc.148A>Cā(p.Lys50Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00025 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.148A>C | p.Lys50Gln | missense_variant | 3/4 | ENST00000304312.5 | |
ATP5ME | NR_033743.2 | n.122A>C | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP5ME | ENST00000304312.5 | c.148A>C | p.Lys50Gln | missense_variant | 3/4 | 1 | NM_007100.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000394 AC: 99AN: 251274Hom.: 0 AF XY: 0.000419 AC XY: 57AN XY: 135888
GnomAD4 exome AF: 0.000252 AC: 369AN: 1461508Hom.: 0 Cov.: 32 AF XY: 0.000249 AC XY: 181AN XY: 727048
GnomAD4 genome AF: 0.000230 AC: 35AN: 152364Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2022 | The c.148A>C (p.K50Q) alteration is located in exon 3 (coding exon 3) of the ATP5I gene. This alteration results from a A to C substitution at nucleotide position 148, causing the lysine (K) at amino acid position 50 to be replaced by a glutamine (Q). 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