19-497985-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_130760.3(MADCAM1):c.205G>T(p.Ala69Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000133 in 1,498,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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.205G>T | p.Ala69Ser | missense_variant | 2/5 | ENST00000215637.8 | |
MADCAM1 | NM_130762.3 | c.205G>T | p.Ala69Ser | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MADCAM1 | ENST00000215637.8 | c.205G>T | p.Ala69Ser | missense_variant | 2/5 | 1 | NM_130760.3 | P2 | |
MADCAM1-AS1 | ENST00000592413.2 | n.542+3556C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 34
GnomAD4 exome AF: 7.43e-7 AC: 1AN: 1346368Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 663910
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2022 | The c.205G>T (p.A69S) alteration is located in exon 2 (coding exon 2) of the MADCAM1 gene. This alteration results from a G to T substitution at nucleotide position 205, causing the alanine (A) at amino acid position 69 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