6-33210005-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_002931.4(RING1):c.330C>T(p.Ile110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,614,216 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0093 ( 11 hom., cov: 32)
Exomes 𝑓: 0.011 ( 120 hom. )
Consequence
RING1
NM_002931.4 synonymous
NM_002931.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.716
Genes affected
RING1 (HGNC:10018): (ring finger protein 1) This gene belongs to the RING finger family, members of which encode proteins characterized by a RING domain, a zinc-binding motif related to the zinc finger domain. The gene product can bind DNA and can act as a transcriptional repressor. It is associated with the multimeric polycomb group protein complex. The gene product interacts with the polycomb group proteins BMI1, EDR1, and CBX4, and colocalizes with these proteins in large nuclear domains. It interacts with the CBX4 protein via its glycine-rich C-terminal domain. The gene maps to the HLA class II region, where it is contiguous with the RING finger genes FABGL and HKE4. [provided by RefSeq, Jul 2008]
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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=-0.39).
BP6
?
Variant 6-33210005-C-T is Benign according to our data. Variant chr6-33210005-C-T is described in ClinVar as [Benign]. Clinvar id is 791566.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
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Synonymous conserved (PhyloP=0.716 with no splicing effect.
BS2
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High AC in GnomAd4 at 1420 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RING1 | NM_002931.4 | c.330C>T | p.Ile110= | synonymous_variant | 4/7 | ENST00000374656.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RING1 | ENST00000374656.5 | c.330C>T | p.Ile110= | synonymous_variant | 4/7 | 1 | NM_002931.4 | P1 | |
RING1 | ENST00000478431.1 | n.318C>T | non_coding_transcript_exon_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00932 AC: 1419AN: 152212Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00863 AC: 2171AN: 251474Hom.: 18 AF XY: 0.00906 AC XY: 1232AN XY: 135916
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GnomAD4 exome AF: 0.0114 AC: 16651AN: 1461886Hom.: 120 Cov.: 32 AF XY: 0.0114 AC XY: 8272AN XY: 727244
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GnomAD4 genome ? AF: 0.00932 AC: 1420AN: 152330Hom.: 11 Cov.: 32 AF XY: 0.00920 AC XY: 685AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | RING1: BP4, BP7, BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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