rs1606388
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_182523.2(CMC1):c.110-22997G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 150,554 control chromosomes in the GnomAD database, including 4,205 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 0.22 ( 4205 hom., cov: 30)
Consequence
CMC1
NM_182523.2 intron
NM_182523.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.260
Genes affected
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CMC1 | NM_182523.2 | c.110-22997G>T | intron_variant | ENST00000466830.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CMC1 | ENST00000466830.6 | c.110-22997G>T | intron_variant | 1 | NM_182523.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.216 AC: 32444AN: 150444Hom.: 4202 Cov.: 30
GnomAD3 genomes
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32444
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150444
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.216 AC: 32469AN: 150554Hom.: 4205 Cov.: 30 AF XY: 0.213 AC XY: 15624AN XY: 73444
GnomAD4 genome
?
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AC:
32469
AN:
150554
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Cov.:
30
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AC XY:
15624
AN XY:
73444
Gnomad4 AFR
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Asia WGS
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AC:
538
AN:
3458
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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