chrX-47624353-C-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001145252.3(CFP):c.1332G>T(p.Gly444=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000704 in 1,207,111 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. G444G) has been classified as Likely benign.
Frequency
Consequence
NM_001145252.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFP | NM_001145252.3 | c.1332G>T | p.Gly444= | synonymous_variant | 9/9 | ENST00000396992.8 | |
CFP | NM_002621.2 | c.1332G>T | p.Gly444= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFP | ENST00000396992.8 | c.1332G>T | p.Gly444= | synonymous_variant | 9/9 | 1 | NM_001145252.3 | P1 | |
CFP | ENST00000247153.7 | c.1332G>T | p.Gly444= | synonymous_variant | 10/10 | 5 | P1 | ||
CFP | ENST00000478222.1 | n.453G>T | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
CFP | ENST00000640573.1 | n.1570G>T | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000448 AC: 49AN: 109452Hom.: 0 Cov.: 22 AF XY: 0.000347 AC XY: 11AN XY: 31700
GnomAD3 exomes AF: 0.000120 AC: 22AN: 183501Hom.: 0 AF XY: 0.0000294 AC XY: 2AN XY: 67931
GnomAD4 exome AF: 0.0000328 AC: 36AN: 1097659Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 10AN XY: 363019
GnomAD4 genome ? AF: 0.000448 AC: 49AN: 109452Hom.: 0 Cov.: 22 AF XY: 0.000347 AC XY: 11AN XY: 31700
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at