GeneBe

rs759951553

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_005811.5(GDF11):​c.99_116delGGCGGCGGCGGCGGCGGC​(p.Ala34_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 0.0000725 in 992,766 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000076 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000072 ( 1 hom. )

Consequence

GDF11
NM_005811.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.25
Variant links:
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]

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ACMG classification

Classification made for transcript

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 11 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GDF11NM_005811.5 linkc.99_116delGGCGGCGGCGGCGGCGGC p.Ala34_Ala39del disruptive_inframe_deletion Exon 1 of 3 ENST00000257868.10 NP_005802.1 O95390A0A024RB20
GDF11XM_006719194.4 linkc.99_116delGGCGGCGGCGGCGGCGGC p.Ala34_Ala39del disruptive_inframe_deletion Exon 1 of 4 XP_006719257.1 O95390A0A024RB20

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GDF11ENST00000257868.10 linkc.99_116delGGCGGCGGCGGCGGCGGC p.Ala34_Ala39del disruptive_inframe_deletion Exon 1 of 3 1 NM_005811.5 ENSP00000257868.5 O95390
GDF11ENST00000546799.1 linkc.15_32delGGCGGCGGCGGCGGCGGC p.Ala6_Ala11del disruptive_inframe_deletion Exon 1 of 4 1 ENSP00000448390.1 H0YI30

Frequencies

GnomAD3 genomes
AF:
0.0000755
AC:
11
AN:
145656
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000739
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000204
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00105
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000720
AC:
61
AN:
847110
Hom.:
1
AF XY:
0.0000965
AC XY:
38
AN XY:
393726
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000919
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000466
Gnomad4 OTH exome
AF:
0.000286
GnomAD4 genome
AF:
0.0000755
AC:
11
AN:
145656
Hom.:
0
Cov.:
30
AF XY:
0.0000707
AC XY:
5
AN XY:
70758
show subpopulations
Gnomad4 AFR
AF:
0.0000739
Gnomad4 AMR
AF:
0.000204
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00105
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs759951553; hg19: chr12-56137184; API