rs9290003
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_028357.1(TMEM30CP):n.56-1792T>C 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 0.496 in 152,058 control chromosomes in the GnomAD database, including 19,001 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 0.50 ( 19001 hom., cov: 32)
Consequence
TMEM30CP
NR_028357.1 intron, non_coding_transcript
NR_028357.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.16
Genes affected
TMEM30CP (HGNC:30443): (transmembrane protein 30C, pseudogene) Predicted to be involved in phospholipid translocation. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus; endoplasmic reticulum; and plasma membrane. [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=-0.99).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM30CP | NR_028357.1 | n.56-1792T>C | intron_variant, non_coding_transcript_variant | ||||
TMEM30CP | NR_028358.1 | n.56-1792T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM30CP | ENST00000489487.1 | n.56-1792T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
TMEM30CP | ENST00000637814.1 | n.193-1792T>C | intron_variant, non_coding_transcript_variant | ||||||
ENST00000654821.1 | n.196-36199A>G | intron_variant, non_coding_transcript_variant | |||||||
TMEM30CP | ENST00000476804.2 | n.56-1792T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.496 AC: 75305AN: 151940Hom.: 18970 Cov.: 32
GnomAD3 genomes
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151940
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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: 0.496 AC: 75388AN: 152058Hom.: 19001 Cov.: 32 AF XY: 0.500 AC XY: 37155AN XY: 74316
GnomAD4 genome
?
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75388
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152058
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32
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37155
AN XY:
74316
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1687
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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