12-55743400-CGCGGCGGCGGCGGCGGCG-CGCGGCG

Variant names:

• chr12-55743400-CGCGGCGGCGGCG-C
• rs759951553
• NM_005811.5:c.105_116delGGCGGCGGCGGC

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3 BS2

The NM_005811.5(GDF11):​c.105_116delGGCGGCGGCGGC​(p.Ala36_Ala39del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000896 in 992,860 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000089 (0 hom., cov: 30)
  • Exomes 𝑓: 0.000090 (0 hom.)
• Consequence: GDF11 NM_005811.5 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25

Genes affected

GDF11 (HGNC:4216): (growth differentiation factor 11) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein plays a role in the development of the nervous and other organ systems, and may regulate aging. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_005811.5
• BS2: High AC in GnomAd4 at 13 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GDF11	NM_005811.5	c.105_116delGGCGGCGGCGGC	p.Ala36_Ala39del	disruptive_inframe_deletion	Exon 1 of 3	ENST00000257868.10	NP_005802.1
GDF11	XM_006719194.4	c.105_116delGGCGGCGGCGGC	p.Ala36_Ala39del	disruptive_inframe_deletion	Exon 1 of 4		XP_006719257.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDF11	ENST00000257868.10	c.105_116delGGCGGCGGCGGC	p.Ala36_Ala39del	disruptive_inframe_deletion	Exon 1 of 3	1	NM_005811.5	ENSP00000257868.5
GDF11	ENST00000546799.1	c.21_32delGGCGGCGGCGGC	p.Ala8_Ala11del	disruptive_inframe_deletion	Exon 1 of 4	1		ENSP00000448390.1

Frequencies

GnomAD3 genomes AF: 0.0000893 AC: 13 AN: 145654 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000739

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000679

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000795

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000610

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000897 AC: 76 AN: 847106 Hom.: 0 AF XY: 0.000102 AC XY: 40 AN XY: 393724

Gnomad4 AFR exome AF: 0.000313

Gnomad4 AMR exome AF: 0.000707

Gnomad4 ASJ exome AF: 0.000185

Gnomad4 EAS exome AF: 0.000732

Gnomad4 SAS exome AF: 0.000345

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000739

Gnomad4 OTH exome AF: 0.0000357

GnomAD4 genome AF: 0.0000892 AC: 13 AN: 145754 Hom.: 0 Cov.: 30 AF XY: 0.000127 AC XY: 9 AN XY: 70870

Gnomad4 AFR AF: 0.0000737

Gnomad4 AMR AF: 0.0000678

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000797

Gnomad4 SAS AF: 0.000210

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000610

Gnomad4 OTH AF: 0.00

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: rs759951553; hg19: chr12-56137184;