15-32732254-T-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013372.7(GREM1):c.*1009T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 236,964 control chromosomes in the GnomAD database, including 11,965 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 8149 hom., cov: 32)
Exomes 𝑓: 0.30 ( 3816 hom. )
Consequence
GREM1
NM_013372.7 3_prime_UTR
NM_013372.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.434
Genes affected
GREM1 (HGNC:2001): (gremlin 1, DAN family BMP antagonist) This gene encodes a member of the BMP (bone morphogenic protein) antagonist family. Like BMPs, BMP antagonists contain cystine knots and typically form homo- and heterodimers. The CAN (cerberus and dan) subfamily of BMP antagonists, to which this gene belongs, is characterized by a C-terminal cystine knot with an eight-membered ring. The antagonistic effect of the secreted glycosylated protein encoded by this gene is likely due to its direct binding to BMP proteins. As an antagonist of BMP, this gene may play a role in regulating organogenesis, body patterning, and tissue differentiation. In mouse, this protein has been shown to relay the sonic hedgehog (SHH) signal from the polarizing region to the apical ectodermal ridge during limb bud outgrowth. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GREM1 | NM_013372.7 | c.*1009T>G | 3_prime_UTR_variant | Exon 2 of 2 | ENST00000651154.1 | NP_037504.1 | ||
GREM1 | NM_001368719.1 | c.*1009T>G | 3_prime_UTR_variant | Exon 2 of 2 | NP_001355648.1 | |||
GREM1 | NM_001191323.2 | c.*1009T>G | 3_prime_UTR_variant | Exon 3 of 3 | NP_001178252.1 | |||
GREM1 | NM_001191322.2 | c.*1009T>G | 3_prime_UTR_variant | Exon 3 of 3 | NP_001178251.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GREM1 | ENST00000651154.1 | c.*1009T>G | 3_prime_UTR_variant | Exon 2 of 2 | NM_013372.7 | ENSP00000498748.1 | ||||
GREM1 | ENST00000652365.1 | c.*1009T>G | 3_prime_UTR_variant | Exon 2 of 2 | ENSP00000498763.1 | |||||
GREM1 | ENST00000560830.1 | c.*1009T>G | 3_prime_UTR_variant | Exon 3 of 3 | 2 | ENSP00000453141.1 |
Frequencies
GnomAD3 genomes AF: 0.322 AC: 48909AN: 151834Hom.: 8145 Cov.: 32
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GnomAD4 exome AF: 0.296 AC: 25170AN: 85012Hom.: 3816 Cov.: 0 AF XY: 0.293 AC XY: 11566AN XY: 39488
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GnomAD4 genome AF: 0.322 AC: 48945AN: 151952Hom.: 8149 Cov.: 32 AF XY: 0.321 AC XY: 23811AN XY: 74254
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at