rs35943942

Positions:

• chr15-32729855-T-TAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_013372.7(GREM1):​c.-1-835_-1-834insAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GREM1 NM_013372.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914

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]

ACMG classification

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
GREM1	NM_013372.7	c.-1-835_-1-834insAA		intron_variant		ENST00000651154.1	NP_037504.1
GREM1	NM_001191322.2	c.-1-835_-1-834insAA		intron_variant			NP_001178251.1
GREM1	NM_001191323.2	c.-1-835_-1-834insAA		intron_variant			NP_001178252.1
GREM1	NM_001368719.1	c.-1-835_-1-834insAA		intron_variant			NP_001355648.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GREM1	ENST00000651154.1	c.-1-835_-1-834insAA		intron_variant			NM_013372.7	ENSP00000498748	P1
GREM1	ENST00000560677.5	c.-1-835_-1-834insAA		intron_variant		4		ENSP00000453387
GREM1	ENST00000560830.1	c.-1-835_-1-834insAA		intron_variant		2		ENSP00000453141
GREM1	ENST00000652365.1	c.-1-835_-1-834insAA		intron_variant				ENSP00000498763	P1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35943942; hg19: chr15-33022056;