rs7626978
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_130384.3(ATRIP):c.1975-150T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 938,796 control chromosomes in the GnomAD database, including 482 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.035 ( 291 hom., cov: 33)
Exomes 𝑓: 0.0054 ( 191 hom. )
Consequence
ATRIP
NM_130384.3 intron
NM_130384.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.730
Genes affected
ATRIP (HGNC:33499): (ATR interacting protein) This gene encodes an essential component of the DNA damage checkpoint. The encoded protein binds to single-stranded DNA coated with replication protein A. The protein also interacts with the ataxia telangiectasia and Rad3 related protein kinase, resulting in its accumulation at intranuclear foci induced by DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 3-48464432-T-G is Benign according to our data. Variant chr3-48464432-T-G is described in ClinVar as [Benign]. Clinvar id is 1238999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATRIP | NM_130384.3 | c.1975-150T>G | intron_variant | ENST00000320211.10 | NP_569055.1 | |||
ATRIP-TREX1 | NR_153405.1 | n.2127-150T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATRIP | ENST00000320211.10 | c.1975-150T>G | intron_variant | 1 | NM_130384.3 | ENSP00000323099 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0348 AC: 5298AN: 152160Hom.: 283 Cov.: 33
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GnomAD4 exome AF: 0.00542 AC: 4261AN: 786518Hom.: 191 AF XY: 0.00484 AC XY: 1966AN XY: 406596
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GnomAD4 genome AF: 0.0351 AC: 5340AN: 152278Hom.: 291 Cov.: 33 AF XY: 0.0348 AC XY: 2593AN XY: 74472
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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