chr6-125889559-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM1BP4_Strong
The NM_181782.5(NCOA7):c.1505C>T(p.Ser502Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S502S) has been classified as Likely benign.
Frequency
Consequence
NM_181782.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCOA7 | ENST00000392477.7 | c.1505C>T | p.Ser502Leu | missense_variant | Exon 9 of 16 | 1 | NM_181782.5 | ENSP00000376269.2 | ||
NCOA7 | ENST00000368357.7 | c.1505C>T | p.Ser502Leu | missense_variant | Exon 10 of 17 | 1 | ENSP00000357341.3 | |||
NCOA7 | ENST00000229634.13 | c.1160C>T | p.Ser387Leu | missense_variant | Exon 8 of 15 | 2 | ENSP00000229634.9 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000959 AC: 24AN: 250344 AF XY: 0.0000665 show subpopulations
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461692Hom.: 0 Cov.: 34 AF XY: 0.0000179 AC XY: 13AN XY: 727144 show subpopulations
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74248 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1505C>T (p.S502L) alteration is located in exon 11 (coding exon 8) of the NCOA7 gene. This alteration results from a C to T substitution at nucleotide position 1505, causing the serine (S) at amino acid position 502 to be replaced by a leucine (L). 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