chr16-50314038-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001114.5(ADCY7):c.2832C>T(p.Ser944=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,614,120 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0090 ( 22 hom., cov: 33)
Exomes 𝑓: 0.00091 ( 15 hom. )
Consequence
ADCY7
NM_001114.5 synonymous
NM_001114.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.705
Genes affected
ADCY7 (HGNC:238): (adenylate cyclase 7) This gene encodes a membrane-bound adenylate cyclase that catalyses the formation of cyclic AMP from ATP and is inhibitable by calcium. The product of this gene is a member of the adenylyl cyclase class-4/guanylyl cyclase enzyme family that is characterized by the presence of twelve membrane-spanning domains in its sequences. Several transcript variants have been observed for this gene, but the full-length natures of only two have been determined so far. [provided by RefSeq, Oct 2013]
BRD7 (HGNC:14310): (bromodomain containing 7) This gene encodes a protein which is a member of the bromodomain-containing protein family. The product of this gene has been identified as a component of one form of the SWI/SNF chromatin remodeling complex, and as a protein which interacts with p53 and is required for p53-dependent oncogene-induced senescence which prevents tumor growth. Pseudogenes have been described on chromosomes 2, 3, 6, 13 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 16-50314038-C-T is Benign according to our data. Variant chr16-50314038-C-T is described in ClinVar as [Benign]. Clinvar id is 768778.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.705 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00898 (1368/152344) while in subpopulation AFR AF= 0.0309 (1285/41572). AF 95% confidence interval is 0.0295. There are 22 homozygotes in gnomad4. There are 672 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY7 | NM_001114.5 | c.2832C>T | p.Ser944= | synonymous_variant | 23/26 | ENST00000673801.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY7 | ENST00000673801.1 | c.2832C>T | p.Ser944= | synonymous_variant | 23/26 | NM_001114.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00897 AC: 1366AN: 152226Hom.: 22 Cov.: 33
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GnomAD3 exomes AF: 0.00243 AC: 610AN: 251252Hom.: 10 AF XY: 0.00163 AC XY: 221AN XY: 135780
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GnomAD4 exome AF: 0.000913 AC: 1335AN: 1461776Hom.: 15 Cov.: 31 AF XY: 0.000804 AC XY: 585AN XY: 727174
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GnomAD4 genome ? AF: 0.00898 AC: 1368AN: 152344Hom.: 22 Cov.: 33 AF XY: 0.00902 AC XY: 672AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational 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