NM_013372.7:c.-2+5040A>G

Variant names:

• chr15-32723201-A-G
• rs7497354
• NM_013372.7:c.-2+5040A>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_013372.7(GREM1):​c.-2+5040A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,034 control chromosomes in the GnomAD database, including 8,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.31 (8242 hom., cov: 32)
• Consequence: GREM1 NM_013372.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.156
• Publications: 5 publications found

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]

GREM1 Gene-Disease associations (from GenCC):

• hereditary mixed polyposis syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet, G2P
• polyposis syndrome, hereditary mixed, 1

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 15-32723201-A-G is Benign according to our data. Variant chr15-32723201-A-G is described in ClinVar as Benign. ClinVar VariationId is 1263209.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013372.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GREM1	NM_013372.7	MANE Select	c.-2+5040A>G		intron	N/A	NP_037504.1
	GREM1	NM_001368719.1		c.-2+4499A>G		intron	N/A	NP_001355648.1
	GREM1	NM_001191323.2		c.-2+5040A>G		intron	N/A	NP_001178252.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GREM1	ENST00000651154.1	MANE Select	c.-2+5040A>G		intron	N/A	ENSP00000498748.1
	GREM1	ENST00000560677.5	TSL:4	c.-2+5040A>G		intron	N/A	ENSP00000453387.1
	GREM1	ENST00000652365.1		c.-2+4499A>G		intron	N/A	ENSP00000498763.1

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47795 AN: 151916 Hom.: 8239 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.314 AC: 47806 AN: 152034 Hom.: 8242 Cov.: 32 AF XY: 0.311 AC XY: 23110 AN XY: 74318

African (AFR) AF: 0.204 AC: 8466 AN: 41496

American (AMR) AF: 0.345 AC: 5268 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3470

East Asian (EAS) AF: 0.0419 AC: 217 AN: 5184

South Asian (SAS) AF: 0.235 AC: 1131 AN: 4818

European-Finnish (FIN) AF: 0.317 AC: 3343 AN: 10534

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26635 AN: 67946

Other (OTH) AF: 0.337 AC: 712 AN: 2114

Alfa AF: 0.375 Hom.: 5656

Bravo AF: 0.313

Asia WGS AF: 0.137 AC: 481 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7497354; hg19: chr15-33015402;