chr19-504774-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_130760.3(MADCAM1):c.958G>A(p.Ala320Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,608,604 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_130760.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MADCAM1 | NM_130760.3 | c.958G>A | p.Ala320Thr | missense_variant | 5/5 | ENST00000215637.8 | |
MADCAM1-AS1 | XR_936221.4 | n.514+2602C>T | intron_variant, non_coding_transcript_variant | ||||
MADCAM1 | NM_130762.3 | c.697G>A | p.Ala233Thr | missense_variant | 4/4 | ||
MADCAM1-AS1 | XR_007067073.1 | n.514+2602C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MADCAM1 | ENST00000215637.8 | c.958G>A | p.Ala320Thr | missense_variant | 5/5 | 1 | NM_130760.3 | P2 | |
MADCAM1-AS1 | ENST00000592413.2 | n.458+2602C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152202Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000217 AC: 54AN: 248914Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135028
GnomAD4 exome AF: 0.000108 AC: 158AN: 1456284Hom.: 0 Cov.: 30 AF XY: 0.0000968 AC XY: 70AN XY: 723444
GnomAD4 genome ? AF: 0.000295 AC: 45AN: 152320Hom.: 1 Cov.: 31 AF XY: 0.000336 AC XY: 25AN XY: 74488
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at