chr6-125889687-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_181782.5(NCOA7):c.1633T>A(p.Leu545Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,614,064 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_181782.5 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 |
---|---|---|---|---|---|---|---|
NCOA7 | NM_181782.5 | c.1633T>A | p.Leu545Ile | missense_variant | 9/16 | ENST00000392477.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA7 | ENST00000392477.7 | c.1633T>A | p.Leu545Ile | missense_variant | 9/16 | 1 | NM_181782.5 | ||
NCOA7 | ENST00000368357.7 | c.1633T>A | p.Leu545Ile | missense_variant | 10/17 | 1 | |||
NCOA7 | ENST00000229634.13 | c.1288T>A | p.Leu430Ile | missense_variant | 8/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250240Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135524
GnomAD4 exome AF: 0.000123 AC: 180AN: 1461790Hom.: 0 Cov.: 34 AF XY: 0.000120 AC XY: 87AN XY: 727178
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.1633T>A (p.L545I) alteration is located in exon 11 (coding exon 8) of the NCOA7 gene. This alteration results from a T to A substitution at nucleotide position 1633, causing the leucine (L) at amino acid position 545 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