16-89645971-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001083314.4(CHMP1A):c.666G>A(p.Ala222Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00401 in 1,611,724 control chromosomes in the GnomAD database, including 216 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001083314.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHMP1A | NM_002768.5 | c.*95G>A | 3_prime_UTR_variant | Exon 7 of 7 | ENST00000397901.8 | NP_002759.2 | ||
CHMP1A | NM_001083314.4 | c.666G>A | p.Ala222Ala | synonymous_variant | Exon 6 of 6 | NP_001076783.1 | ||
CHMP1A | XM_047434195.1 | c.*95G>A | 3_prime_UTR_variant | Exon 7 of 7 | XP_047290151.1 | |||
CHMP1A | NR_046418.3 | n.974G>A | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0217 AC: 3307AN: 152202Hom.: 110 Cov.: 33
GnomAD3 exomes AF: 0.00521 AC: 1271AN: 244026Hom.: 45 AF XY: 0.00390 AC XY: 520AN XY: 133242
GnomAD4 exome AF: 0.00216 AC: 3157AN: 1459404Hom.: 107 Cov.: 31 AF XY: 0.00190 AC XY: 1380AN XY: 725970
GnomAD4 genome AF: 0.0217 AC: 3310AN: 152320Hom.: 109 Cov.: 33 AF XY: 0.0211 AC XY: 1573AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
- -
CHMP1A-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at