19-501698-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130760.3(MADCAM1):c.697C>T(p.Pro233Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000728 in 1,373,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_130760.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MADCAM1 | NM_130760.3 | c.697C>T | p.Pro233Ser | missense_variant | 4/5 | ENST00000215637.8 | |
MADCAM1-AS1 | XR_936221.4 | n.515-74G>A | intron_variant, non_coding_transcript_variant | ||||
MADCAM1 | NM_130762.3 | c.667+2873C>T | intron_variant | ||||
MADCAM1-AS1 | XR_007067073.1 | n.515-74G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MADCAM1 | ENST00000215637.8 | c.697C>T | p.Pro233Ser | missense_variant | 4/5 | 1 | NM_130760.3 | P2 | |
MADCAM1-AS1 | ENST00000592413.2 | n.459-74G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000808 AC: 2AN: 247460Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134376
GnomAD4 exome AF: 7.28e-7 AC: 1AN: 1373150Hom.: 0 Cov.: 35 AF XY: 0.00000147 AC XY: 1AN XY: 680068
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.697C>T (p.P233S) alteration is located in exon 4 (coding exon 4) of the MADCAM1 gene. This alteration results from a C to T substitution at nucleotide position 697, causing the proline (P) at amino acid position 233 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