rs6860
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002768.5(CHMP1A):c.*1354G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,246 control chromosomes in the GnomAD database, including 10,112 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 0.32 ( 10103 hom., cov: 33)
Exomes 𝑓: 0.40 ( 9 hom. )
Consequence
CHMP1A
NM_002768.5 3_prime_UTR
NM_002768.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.43
Genes affected
CHMP1A (HGNC:8740): (charged multivesicular body protein 1A) This gene encodes a member of the CHMP/Chmp family of proteins which are involved in multivesicular body sorting of proteins to the interiors of lysosomes. The initial prediction of the protein sequence encoded by this gene suggested that the encoded protein was a metallopeptidase. The nomenclature has been updated recently to reflect the correct biological function of this encoded protein. Several transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHMP1A | NM_002768.5 | c.*1354G>A | 3_prime_UTR_variant | 7/7 | ENST00000397901.8 | ||
CHMP1A | NM_001083314.4 | c.*1202G>A | 3_prime_UTR_variant | 6/6 | |||
CHMP1A | XM_047434195.1 | c.*1354G>A | 3_prime_UTR_variant | 7/7 | |||
CHMP1A | NR_046418.3 | n.2233G>A | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHMP1A | ENST00000397901.8 | c.*1354G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_002768.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.319 AC: 48563AN: 152018Hom.: 10103 Cov.: 33
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GnomAD4 exome AF: 0.400 AC: 44AN: 110Hom.: 9 Cov.: 0 AF XY: 0.461 AC XY: 35AN XY: 76
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GnomAD4 genome ? AF: 0.319 AC: 48555AN: 152136Hom.: 10103 Cov.: 33 AF XY: 0.314 AC XY: 23380AN XY: 74368
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at