X-100826656-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001325.3(CSTF2):c.725C>T(p.Ala242Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000182 in 1,096,990 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSTF2 | NM_001325.3 | c.725C>T | p.Ala242Val | missense_variant | Exon 7 of 14 | ENST00000372972.7 | NP_001316.1 | |
CSTF2 | NM_001306206.2 | c.725C>T | p.Ala242Val | missense_variant | Exon 7 of 15 | NP_001293135.1 | ||
CSTF2 | XM_047441854.1 | c.725C>T | p.Ala242Val | missense_variant | Exon 7 of 10 | XP_047297810.1 | ||
CSTF2 | NM_001306209.2 | c.703-29C>T | intron_variant | Intron 6 of 13 | NP_001293138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSTF2 | ENST00000372972.7 | c.725C>T | p.Ala242Val | missense_variant | Exon 7 of 14 | 1 | NM_001325.3 | ENSP00000362063.2 | ||
CSTF2 | ENST00000415585.7 | c.725C>T | p.Ala242Val | missense_variant | Exon 7 of 15 | 1 | ENSP00000387996.2 | |||
CSTF2 | ENST00000475126.5 | n.703-29C>T | intron_variant | Intron 6 of 13 | 5 | ENSP00000432060.1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183185Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67643
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1096990Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 362492
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.725C>T (p.A242V) alteration is located in exon 7 (coding exon 7) of the CSTF2 gene. This alteration results from a C to T substitution at nucleotide position 725, causing the alanine (A) at amino acid position 242 to be replaced by a valine (V). 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