rs7767017
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_152435.1(CCDC162P):n.867+207A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,052 control chromosomes in the GnomAD database, including 8,479 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 0.27 ( 8479 hom., cov: 32)
Consequence
CCDC162P
NR_152435.1 intron, non_coding_transcript
NR_152435.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.102
Genes affected
CCDC162P (HGNC:21565): (coiled-coil domain containing 162, pseudogene) This gene is the ortholog of the mouse coiled-coil domain containing 162 gene. This locus is transcribed, but is represented as a unitary pseudogene because there are multiple changes in the coding sequence, including multiple changes that result in premature stop codons, relative to the mouse coding sequence. Transcripts from this locus are expected to encode truncated proteins, and may be candidates for nonsense-mediated decay (NMD). [provided by RefSeq, Sep 2018]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC162P | NR_152435.1 | n.867+207A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC162P | ENST00000368966.10 | n.784+207A>G | intron_variant, non_coding_transcript_variant | ||||||
ENST00000640771.1 | n.865+207A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.268 AC: 40773AN: 151934Hom.: 8461 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.269 AC: 40835AN: 152052Hom.: 8479 Cov.: 32 AF XY: 0.268 AC XY: 19922AN XY: 74336
GnomAD4 genome
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19922
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792
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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