chr13-30921792-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032849.4(MEDAG):āc.733C>Gā(p.Pro245Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,612,606 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 32)
Exomes š: 0.000012 ( 0 hom. )
Consequence
MEDAG
NM_032849.4 missense
NM_032849.4 missense
Scores
2
10
7
Clinical Significance
Conservation
PhyloP100: 4.70
Genes affected
MEDAG (HGNC:25926): (mesenteric estrogen dependent adipogenesis) Predicted to be involved in positive regulation of fat cell differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEDAG | NM_032849.4 | c.733C>G | p.Pro245Ala | missense_variant | 4/5 | ENST00000380482.9 | NP_116238.3 | |
TEX26-AS1 | NR_038287.1 | n.1437+9009G>C | intron_variant, non_coding_transcript_variant | |||||
MEDAG | XM_017020801.2 | c.280C>G | p.Pro94Ala | missense_variant | 3/4 | XP_016876290.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEDAG | ENST00000380482.9 | c.733C>G | p.Pro245Ala | missense_variant | 4/5 | 1 | NM_032849.4 | ENSP00000369849 | P1 | |
TEX26-AS1 | ENST00000585870.6 | n.1437+9009G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000800 AC: 2AN: 249930Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135020
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460464Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726398
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74324
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.733C>G (p.P245A) alteration is located in exon 4 (coding exon 4) of the MEDAG gene. This alteration results from a C to G substitution at nucleotide position 733, causing the proline (P) at amino acid position 245 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of loop (P = 9e-04);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at