X-73447542-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005193.2(CDX4):c.289C>T(p.Pro97Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000116 in 1,209,659 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005193.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 112037Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34199
GnomAD3 exomes AF: 0.0000219 AC: 4AN: 182478Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67128
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097622Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 362996
GnomAD4 genome AF: 0.0000357 AC: 4AN: 112037Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34199
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.289C>T (p.P97S) alteration is located in exon 1 (coding exon 1) of the CDX4 gene. This alteration results from a C to T substitution at nucleotide position 289, causing the proline (P) at amino acid position 97 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