NM_001190787.3:c.120+3G>A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4BP6BS1BS2
The NM_001190787.3(MCIDAS):c.120+3G>A variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0045 in 1,520,420 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001190787.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCIDAS | ENST00000513312.3 | c.120+3G>A | splice_region_variant, intron_variant | Intron 1 of 6 | 1 | NM_001190787.3 | ENSP00000426359.1 | |||
MCIDAS | ENST00000513468.5 | n.120+3G>A | splice_region_variant, intron_variant | Intron 1 of 6 | 5 | ENSP00000422165.1 | ||||
MCIDAS | ENST00000515336.1 | n.58-85G>A | intron_variant | Intron 1 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00351 AC: 534AN: 152210Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00501 AC: 563AN: 112322Hom.: 5 AF XY: 0.00521 AC XY: 325AN XY: 62370
GnomAD4 exome AF: 0.00461 AC: 6309AN: 1368092Hom.: 31 Cov.: 32 AF XY: 0.00483 AC XY: 3259AN XY: 675090
GnomAD4 genome AF: 0.00349 AC: 532AN: 152328Hom.: 5 Cov.: 33 AF XY: 0.00344 AC XY: 256AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:2
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MCIDAS: BP4, BS2 -
Ciliary dyskinesia, primary, 42 Uncertain:1
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Primary ciliary dyskinesia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at