rs11169974
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_004302.5(ACVR1B):c.*2402C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 152,746 control chromosomes in the GnomAD database, including 66 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 0.028 ( 66 hom., cov: 32)
Exomes 𝑓: 0.021 ( 0 hom. )
Consequence
ACVR1B
NM_004302.5 3_prime_UTR
NM_004302.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.79
Genes affected
ACVR1B (HGNC:172): (activin A receptor type 1B) This gene encodes an activin A type IB receptor. Activins are dimeric growth and differentiation factors which belong to the transforming growth factor-beta (TGF-beta) superfamily of structurally related signaling proteins. Activins signal through a heteromeric complex of receptor serine kinases which include at least two type I and two type II receptors. This protein is a type I receptor which is essential for signaling. Mutations in this gene are associated with pituitary tumors. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2010]
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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=-0.81).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0276 (4199/152260) while in subpopulation AFR AF= 0.0387 (1608/41534). AF 95% confidence interval is 0.0371. There are 66 homozygotes in gnomad4. There are 2080 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 4203 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACVR1B | NM_004302.5 | c.*2402C>T | 3_prime_UTR_variant | 9/9 | ENST00000257963.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACVR1B | ENST00000257963.9 | c.*2402C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_004302.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0276 AC: 4203AN: 152142Hom.: 66 Cov.: 32
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GnomAD4 exome AF: 0.0206 AC: 10AN: 486Hom.: 0 Cov.: 0 AF XY: 0.0208 AC XY: 6AN XY: 288
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GnomAD4 genome ? AF: 0.0276 AC: 4199AN: 152260Hom.: 66 Cov.: 32 AF XY: 0.0279 AC XY: 2080AN XY: 74446
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at