chrX-100833191-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001325.3(CSTF2):c.1219C>T(p.Pro407Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000265 in 1,207,666 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001325.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSTF2 | NM_001325.3 | c.1219C>T | p.Pro407Ser | missense_variant | Exon 11 of 14 | ENST00000372972.7 | NP_001316.1 | |
CSTF2 | NM_001306206.2 | c.1279C>T | p.Pro427Ser | missense_variant | Exon 12 of 15 | NP_001293135.1 | ||
CSTF2 | NM_001306209.2 | c.1168C>T | p.Pro390Ser | missense_variant | Exon 11 of 14 | NP_001293138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSTF2 | ENST00000372972.7 | c.1219C>T | p.Pro407Ser | missense_variant | Exon 11 of 14 | 1 | NM_001325.3 | ENSP00000362063.2 | ||
CSTF2 | ENST00000415585.7 | c.1279C>T | p.Pro427Ser | missense_variant | Exon 12 of 15 | 1 | ENSP00000387996.2 | |||
CSTF2 | ENST00000475126.5 | n.1168C>T | non_coding_transcript_exon_variant | Exon 11 of 14 | 5 | ENSP00000432060.1 |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 112133Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34315
GnomAD4 exome AF: 0.0000256 AC: 28AN: 1095533Hom.: 0 Cov.: 31 AF XY: 0.0000305 AC XY: 11AN XY: 361139
GnomAD4 genome AF: 0.0000357 AC: 4AN: 112133Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34315
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1219C>T (p.P407S) alteration is located in exon 11 (coding exon 11) of the CSTF2 gene. This alteration results from a C to T substitution at nucleotide position 1219, causing the proline (P) at amino acid position 407 to be replaced by a serine (S). 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