2-157416069-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004288.5(CYTIP):c.688C>T(p.Pro230Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004288.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYTIP | NM_004288.5 | c.688C>T | p.Pro230Ser | missense_variant | 8/8 | ENST00000264192.8 | |
CYTIP | XM_017005386.3 | c.370C>T | p.Pro124Ser | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYTIP | ENST00000264192.8 | c.688C>T | p.Pro230Ser | missense_variant | 8/8 | 1 | NM_004288.5 | P1 | |
CYTIP | ENST00000418920.5 | c.370C>T | p.Pro124Ser | missense_variant | 9/9 | 5 | |||
CYTIP | ENST00000457793.6 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000243 AC: 61AN: 250682Hom.: 0 AF XY: 0.000207 AC XY: 28AN XY: 135490
GnomAD4 exome AF: 0.000133 AC: 194AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.000140 AC XY: 102AN XY: 727224
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.688C>T (p.P230S) alteration is located in exon 8 (coding exon 8) of the CYTIP gene. This alteration results from a C to T substitution at nucleotide position 688, causing the proline (P) at amino acid position 230 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