chr6-7329865-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001170692.2(CAGE1):c.2462C>T(p.Pro821Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000439 in 1,458,374 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001170692.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAGE1 | NM_001170692.2 | c.2462C>T | p.Pro821Leu | missense_variant | 13/14 | ENST00000502583.6 | NP_001164163.1 | |
CAGE1 | NM_001170693.2 | c.2357C>T | p.Pro786Leu | missense_variant | 12/13 | NP_001164164.1 | ||
CAGE1 | NM_205864.3 | c.1868C>T | p.Pro623Leu | missense_variant | 10/11 | NP_995586.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAGE1 | ENST00000502583.6 | c.2462C>T | p.Pro821Leu | missense_variant | 13/14 | 5 | NM_001170692.2 | ENSP00000425493.1 | ||
CAGE1 | ENST00000338150.8 | c.2357C>T | p.Pro786Leu | missense_variant | 12/13 | 2 | ENSP00000338107.4 | |||
CAGE1 | ENST00000379918.8 | c.2396C>T | p.Pro799Leu | missense_variant | 13/14 | 5 | ENSP00000369250.4 | |||
CAGE1 | ENST00000512086.5 | c.2276C>T | p.Pro759Leu | missense_variant | 11/12 | 5 | ENSP00000427583.1 | |||
CAGE1 | ENST00000296742.11 | c.1868C>T | p.Pro623Leu | missense_variant | 10/11 | 1 | ENSP00000296742.7 | |||
CAGE1 | ENST00000442019.6 | n.*1728C>T | non_coding_transcript_exon_variant | 13/14 | 1 | ENSP00000391746.2 | ||||
CAGE1 | ENST00000458291.6 | n.*414C>T | non_coding_transcript_exon_variant | 13/14 | 1 | ENSP00000390644.2 | ||||
CAGE1 | ENST00000442019.6 | n.*1728C>T | 3_prime_UTR_variant | 13/14 | 1 | ENSP00000391746.2 | ||||
CAGE1 | ENST00000458291.6 | n.*414C>T | 3_prime_UTR_variant | 13/14 | 1 | ENSP00000390644.2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152076Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 26AN: 202688Hom.: 0 AF XY: 0.000129 AC XY: 14AN XY: 108246
GnomAD4 exome AF: 0.0000406 AC: 53AN: 1306180Hom.: 0 Cov.: 19 AF XY: 0.0000429 AC XY: 28AN XY: 652532
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152194Hom.: 1 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.2462C>T (p.P821L) alteration is located in exon 13 (coding exon 12) of the CAGE1 gene. This alteration results from a C to T substitution at nucleotide position 2462, causing the proline (P) at amino acid position 821 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at