X-120874977-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001145718.3(CT47B1):c.694G>T(p.Ala232Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000314 in 1,208,900 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A232T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145718.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000444 AC: 5AN: 112587Hom.: 0 Cov.: 22 AF XY: 0.0000575 AC XY: 2AN XY: 34775
GnomAD3 exomes AF: 0.0000329 AC: 6AN: 182585Hom.: 0 AF XY: 0.0000592 AC XY: 4AN XY: 67553
GnomAD4 exome AF: 0.0000301 AC: 33AN: 1096313Hom.: 0 Cov.: 31 AF XY: 0.0000386 AC XY: 14AN XY: 362289
GnomAD4 genome AF: 0.0000444 AC: 5AN: 112587Hom.: 0 Cov.: 22 AF XY: 0.0000575 AC XY: 2AN XY: 34775
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.694G>T (p.A232S) alteration is located in exon 1 (coding exon 1) of the CT47B1 gene. This alteration results from a G to T substitution at nucleotide position 694, causing the alanine (A) at amino acid position 232 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