chr19-501875-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_130760.3(MADCAM1):c.874C>G(p.Arg292Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000462 in 1,557,552 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_130760.3 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 |
---|---|---|---|---|---|---|---|
MADCAM1 | NM_130760.3 | c.874C>G | p.Arg292Gly | missense_variant | 4/5 | ENST00000215637.8 | |
MADCAM1-AS1 | XR_936221.4 | n.515-251G>C | intron_variant, non_coding_transcript_variant | ||||
MADCAM1 | NM_130762.3 | c.668-2870C>G | intron_variant | ||||
MADCAM1-AS1 | XR_007067073.1 | n.515-251G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MADCAM1 | ENST00000215637.8 | c.874C>G | p.Arg292Gly | missense_variant | 4/5 | 1 | NM_130760.3 | P2 | |
MADCAM1-AS1 | ENST00000592413.2 | n.459-251G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 151924Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000913 AC: 15AN: 164380Hom.: 0 AF XY: 0.000102 AC XY: 9AN XY: 88376
GnomAD4 exome AF: 0.0000434 AC: 61AN: 1405628Hom.: 0 Cov.: 54 AF XY: 0.0000432 AC XY: 30AN XY: 694728
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 151924Hom.: 0 Cov.: 32 AF XY: 0.0000809 AC XY: 6AN XY: 74196
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.874C>G (p.R292G) alteration is located in exon 4 (coding exon 4) of the MADCAM1 gene. This alteration results from a C to G substitution at nucleotide position 874, causing the arginine (R) at amino acid position 292 to be replaced by a glycine (G). 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