4-9782215-C-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_000798.5(DRD5):c.186C>A(p.Cys62Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0004 in 1,611,896 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00021 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00042 ( 13 hom. )
Consequence
DRD5
NM_000798.5 stop_gained
NM_000798.5 stop_gained
Scores
2
5
Clinical Significance
Conservation
PhyloP100: -0.838
Genes affected
DRD5 (HGNC:3026): (dopamine receptor D5) This gene encodes the D5 subtype of the dopamine receptor. The D5 subtype is a G-protein coupled receptor which stimulates adenylyl cyclase. This receptor is expressed in neurons in the limbic regions of the brain. It has a 10-fold higher affinity for dopamine than the D1 subtype. Pseudogenes related to this gene reside on chromosomes 1 and 2. [provided by RefSeq, Jul 2008]
SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
Variant 4-9782215-C-A is Benign according to our data. Variant chr4-9782215-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3043073.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 32 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DRD5 | NM_000798.5 | c.186C>A | p.Cys62Ter | stop_gained | 1/1 | ENST00000304374.4 | NP_000789.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DRD5 | ENST00000304374.4 | c.186C>A | p.Cys62Ter | stop_gained | 1/1 | NM_000798.5 | ENSP00000306129 | P1 | ||
SLC2A9 | ENST00000503803.5 | n.386-2150G>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
SLC2A9 | ENST00000508585.5 | n.182-10846G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152260Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000884 AC: 220AN: 248814Hom.: 4 AF XY: 0.00116 AC XY: 156AN XY: 134644
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GnomAD4 exome AF: 0.000419 AC: 612AN: 1459518Hom.: 13 Cov.: 31 AF XY: 0.000620 AC XY: 450AN XY: 725934
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GnomAD4 genome AF: 0.000210 AC: 32AN: 152378Hom.: 0 Cov.: 34 AF XY: 0.000322 AC XY: 24AN XY: 74514
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
DRD5-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 06, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_addAF
Benign
T
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Benign
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Benign
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Benign
N
MutationTaster
Benign
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Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at