19-498774-G-A

Variant names:

• chr19-498774-G-A
• rs894972910
• NM_130760.3:c.616G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_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
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.70

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]

MADCAM1-AS1 (HGNC:55315): (MADCAM1 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20524803).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MADCAM1	NM_130760.3	c.616G>A	p.Ala206Thr	missense_variant	Exon 3 of 5	ENST00000215637.8	NP_570116.2
MADCAM1	NM_130762.3	c.616G>A	p.Ala206Thr	missense_variant	Exon 3 of 4		NP_570118.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MADCAM1	ENST00000215637.8	c.616G>A	p.Ala206Thr	missense_variant	Exon 3 of 5	1	NM_130760.3	ENSP00000215637.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1351282 Hom.: 0 Cov.: 50 AF XY: 0.00 AC XY: 0 AN XY: 666600

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

Bravo AF: 0.0000227

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 25, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.616G>A (p.A206T) alteration is located in exon 3 (coding exon 3) of the MADCAM1 gene. This alteration results from a G to A substitution at nucleotide position 616, causing the alanine (A) at amino acid position 206 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.48
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.47
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.15	.;T;T;T;.;T;.;.
Eigen	Benign	0.043
Eigen_PC	Benign	0.0035
FATHMM_MKL	Benign	0.57	D
LIST_S2	Uncertain	0.86	D;D;D;D;D;D;D;D
M_CAP	Benign	0.021	T
MetaRNN	Benign	0.21	T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	.;.;.;.;L;L;.;.
PrimateAI	Benign	0.48	T
PROVEAN	Uncertain	-2.6	.;.;.;.;D;N;N;.
REVEL	Benign	0.071
Sift	Benign	0.072	.;.;.;.;T;D;D;.
Sift4G	Uncertain	0.037	D;T;T;T;T;T;T;T
Polyphen		0.99	.;.;.;.;.;D;.;.
Vest4		0.44
MutPred		0.47		Loss of catalytic residue at M208 (P = 0.0233);Loss of catalytic residue at M208 (P = 0.0233);Loss of catalytic residue at M208 (P = 0.0233);Loss of catalytic residue at M208 (P = 0.0233);Loss of catalytic residue at M208 (P = 0.0233);Loss of catalytic residue at M208 (P = 0.0233);.;Loss of catalytic residue at M208 (P = 0.0233);
MVP		0.11
MPC		0.76
ClinPred		0.97	D
GERP RS		3.4
Varity_R		0.40
gMVP		0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs894972910; hg19: chr19-498774;