rs3822908
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001350599.2(MMS22L):c.3482+35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,533,606 control chromosomes in the GnomAD database, including 32,324 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 3018 hom., cov: 32)
Exomes 𝑓: 0.20 ( 29306 hom. )
Consequence
MMS22L
NM_001350599.2 intron
NM_001350599.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.78
Genes affected
MMS22L (HGNC:21475): (MMS22 like, DNA repair protein) The protein encoded by this gene forms a complex with tonsoku-like, DNA repair protein (TONSL), and this complex recognizes and repairs DNA double-strand breaks at sites of stalled or collapsed replication forks. The encoded protein also can bind with the histone-associated protein NFKBIL2 to help regulate the chromatin state at stalled replication forks. Finally, this gene appears to be overexpressed in most lung and esophageal cancers. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMS22L | NM_001350599.2 | c.3482+35A>G | intron_variant | ENST00000683635.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMS22L | ENST00000683635.1 | c.3482+35A>G | intron_variant | NM_001350599.2 | P1 | ||||
MMS22L | ENST00000275053.8 | c.3482+35A>G | intron_variant | 2 | P1 | ||||
MMS22L | ENST00000369251.6 | c.3362+35A>G | intron_variant | 2 | |||||
MMS22L | ENST00000514790.1 | n.176A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.185 AC: 28151AN: 152062Hom.: 3006 Cov.: 32
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GnomAD3 exomes AF: 0.226 AC: 56328AN: 249248Hom.: 7656 AF XY: 0.222 AC XY: 29877AN XY: 134666
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GnomAD4 exome AF: 0.198 AC: 273164AN: 1381426Hom.: 29306 Cov.: 20 AF XY: 0.198 AC XY: 136933AN XY: 691672
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GnomAD4 genome ? AF: 0.185 AC: 28178AN: 152180Hom.: 3018 Cov.: 32 AF XY: 0.188 AC XY: 14000AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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