NM_130760.3:c.616G>A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130760.3(MADCAM1):c.616G>A(p.Ala206Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MADCAM1
NM_130760.3 missense
NM_130760.3 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 3.70
Publications
0 publications found
Genes affected
MADCAM1 (HGNC:6765): (mucosal vascular addressin cell adhesion molecule 1) The protein encoded by this gene is an endothelial cell adhesion molecule that interacts preferentially with the leukocyte beta7 integrin LPAM-1 (alpha4beta7), L-selectin, and VLA-4 (alpha4beta1) on myeloid cells to direct leukocytes into mucosal and inflamed tissues. It is a member of the immunoglobulin family and is similar to ICAM1 and VCAM1. At least seven alternatively spliced transcripts encoding different protein isoforms have been found for this gene, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.20524803).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_130760.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MADCAM1 | TSL:1 MANE Select | c.616G>A | p.Ala206Thr | missense | Exon 3 of 5 | ENSP00000215637.2 | Q13477-1 | ||
| MADCAM1 | TSL:1 | c.616G>A | p.Ala206Thr | missense | Exon 3 of 4 | ENSP00000304247.2 | Q13477-3 | ||
| MADCAM1 | TSL:1 | c.331G>A | p.Ala111Thr | missense | Exon 2 of 3 | ENSP00000372130.4 | Q13477-4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1351282Hom.: 0 Cov.: 50 AF XY: 0.00 AC XY: 0AN XY: 666600
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1351282
Hom.:
Cov.:
50
AF XY:
AC XY:
0
AN XY:
666600
African (AFR)
AF:
AC:
0
AN:
29210
American (AMR)
AF:
AC:
0
AN:
23958
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23458
East Asian (EAS)
AF:
AC:
0
AN:
34980
South Asian (SAS)
AF:
AC:
0
AN:
74516
European-Finnish (FIN)
AF:
AC:
0
AN:
34916
Middle Eastern (MID)
AF:
AC:
0
AN:
5216
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1068752
Other (OTH)
AF:
AC:
0
AN:
56276
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of catalytic residue at M208 (P = 0.0233)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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