chr10-46012911-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001145263.2(NCOA4):c.686C>T(p.Thr229Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0074 in 1,614,104 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001145263.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOA4 | NM_001145263.2 | c.686C>T | p.Thr229Ile | missense_variant | 7/10 | ENST00000581486.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA4 | ENST00000581486.6 | c.686C>T | p.Thr229Ile | missense_variant | 7/10 | 1 | NM_001145263.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00550 AC: 837AN: 152192Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00566 AC: 1422AN: 251246Hom.: 7 AF XY: 0.00572 AC XY: 776AN XY: 135768
GnomAD4 exome AF: 0.00760 AC: 11110AN: 1461794Hom.: 57 Cov.: 30 AF XY: 0.00739 AC XY: 5377AN XY: 727212
GnomAD4 genome ? AF: 0.00549 AC: 836AN: 152310Hom.: 6 Cov.: 32 AF XY: 0.00569 AC XY: 424AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | May 22, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | TIMM23B: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at