chr1-240608860-C-T

Variant names:

• chr1-240608860-C-T
• rs10495473
• NM_022469.4:c.-2+3024G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022469.4(GREM2):​c.-2+3024G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 151,974 control chromosomes in the GnomAD database, including 4,214 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 0.21 (4214 hom., cov: 32)
• Consequence: GREM2 NM_022469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 1 publications found

Genes affected

GREM2 (HGNC:17655): (gremlin 2, 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. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GREM2	NM_022469.4	c.-2+3024G>A		intron_variant	Intron 1 of 1	ENST00000318160.5	NP_071914.3
GREM2	XM_047427832.1	c.-277+3024G>A		intron_variant	Intron 1 of 2		XP_047283788.1
GREM2	XM_047427839.1	c.-366+3024G>A		intron_variant	Intron 1 of 3		XP_047283795.1
GREM2	XM_011544249.3	c.-122+3024G>A		intron_variant	Intron 1 of 2		XP_011542551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GREM2	ENST00000318160.5	c.-2+3024G>A		intron_variant	Intron 1 of 1	1	NM_022469.4	ENSP00000318650.4

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32277 AN: 151856 Hom.: 4216 Cov.: 32

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.212 AC: 32270 AN: 151974 Hom.: 4214 Cov.: 32 AF XY: 0.213 AC XY: 15831 AN XY: 74272

African (AFR) AF: 0.0516 AC: 2141 AN: 41486

American (AMR) AF: 0.241 AC: 3667 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1240 AN: 5124

South Asian (SAS) AF: 0.310 AC: 1490 AN: 4814

European-Finnish (FIN) AF: 0.215 AC: 2269 AN: 10570

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19554 AN: 67952

Other (OTH) AF: 0.247 AC: 521 AN: 2112

Alfa AF: 0.184 Hom.: 595

Bravo AF: 0.207

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.4
DANN	Benign	0.77
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: rs10495473; hg19: chr1-240772160;