rs117732387
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_021930.6(RINT1):c.1471+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00545 in 1,579,480 control chromosomes in the GnomAD database, including 350 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 57 hom., cov: 32)
Exomes 𝑓: 0.0050 ( 293 hom. )
Consequence
RINT1
NM_021930.6 intron
NM_021930.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.291
Genes affected
RINT1 (HGNC:21876): (RAD50 interactor 1) This gene encodes a protein first identified for its ability to interact with the RAD50 double strand break repair protein, with the resulting interaction implicated in the regulation of cell cycle progression and telomere length. The encoded protein may also play a role in trafficking of cellular cargo from the endosome to the trans-Golgi network. Mutations in this gene may be associated with breast cancer in human patients. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 7-105551717-T-C is Benign according to our data. Variant chr7-105551717-T-C is described in ClinVar as [Benign]. Clinvar id is 416391.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RINT1 | NM_021930.6 | c.1471+10T>C | intron_variant | ENST00000257700.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RINT1 | ENST00000257700.7 | c.1471+10T>C | intron_variant | 1 | NM_021930.6 | P1 | |||
RINT1 | ENST00000497979.5 | c.*1076+10T>C | intron_variant, NMD_transcript_variant | 5 | |||||
RINT1 | ENST00000474123.1 | n.475+10T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00987 AC: 1502AN: 152208Hom.: 53 Cov.: 32
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GnomAD3 exomes AF: 0.0163 AC: 3663AN: 224890Hom.: 157 AF XY: 0.0136 AC XY: 1659AN XY: 121948
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GnomAD4 exome AF: 0.00496 AC: 7084AN: 1427154Hom.: 293 Cov.: 27 AF XY: 0.00460 AC XY: 3261AN XY: 709088
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GnomAD4 genome ? AF: 0.00997 AC: 1518AN: 152326Hom.: 57 Cov.: 32 AF XY: 0.0114 AC XY: 849AN XY: 74494
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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 | Feb 01, 2024 | - - |
Computational scores
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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