chr19-501690-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_130760.3(MADCAM1):c.689C>T(p.Pro230Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000878 in 1,595,396 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MADCAM1 | NM_130760.3 | c.689C>T | p.Pro230Leu | missense_variant | 4/5 | ENST00000215637.8 | |
MADCAM1-AS1 | XR_936221.4 | n.515-66G>A | intron_variant, non_coding_transcript_variant | ||||
MADCAM1 | NM_130762.3 | c.667+2865C>T | intron_variant | ||||
MADCAM1-AS1 | XR_007067073.1 | n.515-66G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MADCAM1 | ENST00000215637.8 | c.689C>T | p.Pro230Leu | missense_variant | 4/5 | 1 | NM_130760.3 | P2 | |
MADCAM1-AS1 | ENST00000592413.2 | n.459-66G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000266 AC: 4AN: 150200Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000169 AC: 4AN: 236520Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128344
GnomAD4 exome AF: 0.00000692 AC: 10AN: 1445082Hom.: 0 Cov.: 35 AF XY: 0.00000696 AC XY: 5AN XY: 718344
GnomAD4 genome ? AF: 0.0000266 AC: 4AN: 150314Hom.: 0 Cov.: 31 AF XY: 0.0000408 AC XY: 3AN XY: 73468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.689C>T (p.P230L) 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 689, causing the proline (P) at amino acid position 230 to be replaced by a leucine (L). 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