chr3-151880738-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_033050.6(SUCNR1):c.195C>T(p.Leu65Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,614,080 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0016 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 31 hom. )
Consequence
SUCNR1
NM_033050.6 synonymous
NM_033050.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.367
Genes affected
SUCNR1 (HGNC:4542): (succinate receptor 1) This gene encodes a G-protein-coupled receptor for succinate, an intermediate molecule of the citric acid cycle. It is involved in the promotion of hematopoietic progenitor cell development, and it has a potential role in renovascular hypertension which has known correlations to renal failure, diabetes and atherosclerosis. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 3-151880738-C-T is Benign according to our data. Variant chr3-151880738-C-T is described in ClinVar as [Benign]. Clinvar id is 713065.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.367 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00165 (251/152284) while in subpopulation EAS AF= 0.0374 (194/5188). AF 95% confidence interval is 0.0331. There are 3 homozygotes in gnomad4. There are 146 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUCNR1 | NM_033050.6 | c.195C>T | p.Leu65Leu | synonymous_variant | Exon 3 of 3 | ENST00000362032.6 | NP_149039.2 | |
AADACL2-AS1 | NR_110202.1 | n.319+47119G>A | intron_variant | Intron 1 of 3 | ||||
AADACL2-AS1 | NR_110203.1 | n.319+47119G>A | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUCNR1 | ENST00000362032.6 | c.195C>T | p.Leu65Leu | synonymous_variant | Exon 3 of 3 | 1 | NM_033050.6 | ENSP00000355156.4 | ||
AADACL2-AS1 | ENST00000475855.1 | n.319+47119G>A | intron_variant | Intron 1 of 3 | 5 | |||||
AADACL2-AS1 | ENST00000483843.6 | n.439+36877G>A | intron_variant | Intron 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00166 AC: 253AN: 152166Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00363 AC: 913AN: 251284Hom.: 15 AF XY: 0.00370 AC XY: 502AN XY: 135814
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GnomAD4 exome AF: 0.00144 AC: 2103AN: 1461796Hom.: 31 Cov.: 33 AF XY: 0.00160 AC XY: 1162AN XY: 727200
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GnomAD4 genome AF: 0.00165 AC: 251AN: 152284Hom.: 3 Cov.: 32 AF XY: 0.00196 AC XY: 146AN XY: 74466
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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
May 18, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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