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GeneBe

rs143383

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000557.5(GDF5):c.-275C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151770 control chromosomes in the gnomAD Genomes database, including 21153 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 0.48 ( 21153 hom., cov: 30)

Consequence

GDF5
NM_000557.5 5_prime_UTR

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.46

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GDF5NM_000557.5 linkuse as main transcriptc.-275C>T 5_prime_UTR_variant 1/2 ENST00000374369.8
GDF5NM_001319138.2 linkuse as main transcriptc.-241-34C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GDF5ENST00000374369.8 linkuse as main transcriptc.-275C>T 5_prime_UTR_variant 1/21 NM_000557.5 P1
GDF5ENST00000374372.1 linkuse as main transcriptc.-241-34C>T intron_variant 1 P1

Frequencies

GnomAD3 genomes
AF:
0.477
AC:
72469
AN:
151770
Hom.:
21153
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.121
Gnomad AMI
AF:
0.599
Gnomad AMR
AF:
0.624
Gnomad ASJ
AF:
0.545
Gnomad EAS
AF:
0.717
Gnomad SAS
AF:
0.441
Gnomad FIN
AF:
0.585
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.623
Gnomad OTH
AF:
0.515
GnomAD4 exome
AF:
0.590
AC:
214796
AN:
363806
Hom.:
65940
AF XY:
0.583
AC XY:
111720
AN XY:
191776
show subpopulations
Gnomad4 AFR exome
AF:
0.123
Gnomad4 AMR exome
AF:
0.683
Gnomad4 ASJ exome
AF:
0.550
Gnomad4 EAS exome
AF:
0.748
Gnomad4 SAS exome
AF:
0.450
Gnomad4 FIN exome
AF:
0.587
Gnomad4 NFE exome
AF:
0.621
Gnomad4 OTH exome
AF:
0.574
Alfa
AF:
0.608
Hom.:
40102
Bravo
AF:
0.473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
21

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: rs143383; hg19: chr20-34025983; API