rs2766543
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001286574.2(ARMC12):c.444+2339G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 150,708 control chromosomes in the GnomAD database, including 27,004 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 0.58 ( 27004 hom., cov: 28)
Consequence
ARMC12
NM_001286574.2 intron
NM_001286574.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.39
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=-1.01).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMC12 | NM_001286574.2 | c.444+2339G>T | intron_variant | ENST00000373866.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC12 | ENST00000373866.4 | c.444+2339G>T | intron_variant | 3 | NM_001286574.2 | A1 | |||
ARMC12 | ENST00000288065.6 | c.525+2339G>T | intron_variant | 1 | P3 | ||||
ARMC12 | ENST00000373869.7 | c.444+2339G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.583 AC: 87848AN: 150590Hom.: 26943 Cov.: 28
GnomAD3 genomes
?
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87848
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150590
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28
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.584 AC: 87968AN: 150708Hom.: 27004 Cov.: 28 AF XY: 0.582 AC XY: 42739AN XY: 73444
GnomAD4 genome
?
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AC:
87968
AN:
150708
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28
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42739
AN XY:
73444
Gnomad4 AFR
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Asia WGS
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1869
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3478
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