rs2236575
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022362.5(MMS19):c.1607-27A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 1,612,030 control chromosomes in the GnomAD database, including 145,455 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 0.40 ( 12290 hom., cov: 33)
Exomes 𝑓: 0.43 ( 133165 hom. )
Consequence
MMS19
NM_022362.5 intron
NM_022362.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0910
Genes affected
MMS19 (HGNC:13824): (MMS19 homolog, cytosolic iron-sulfur assembly component) Enables estrogen receptor binding activity and transcription coactivator activity. Involved in several processes, including iron-sulfur cluster assembly; positive regulation of nucleobase-containing compound metabolic process; and protein maturation by iron-sulfur cluster transfer. Located in cytosol; nucleoplasm; and spindle. Part of CIA complex and MMXD complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMS19 | NM_022362.5 | c.1607-27A>T | intron_variant | ENST00000438925.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMS19 | ENST00000438925.7 | c.1607-27A>T | intron_variant | 1 | NM_022362.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.402 AC: 61071AN: 151918Hom.: 12292 Cov.: 33
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GnomAD3 exomes AF: 0.420 AC: 104565AN: 249192Hom.: 22313 AF XY: 0.418 AC XY: 56207AN XY: 134604
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GnomAD4 exome AF: 0.426 AC: 621496AN: 1459994Hom.: 133165 Cov.: 36 AF XY: 0.424 AC XY: 307699AN XY: 726262
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GnomAD4 genome ? AF: 0.402 AC: 61085AN: 152036Hom.: 12290 Cov.: 33 AF XY: 0.399 AC XY: 29617AN XY: 74302
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
La Branchor
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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