chr14-57233861-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006544.4(EXOC5):c.737T>C(p.Ile246Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,610,574 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I246V) has been classified as Uncertain significance.
Frequency
Consequence
NM_006544.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOC5 | NM_006544.4 | c.737T>C | p.Ile246Thr | missense_variant | 9/18 | ENST00000621441.5 | |
EXOC5 | XM_005267272.4 | c.851T>C | p.Ile284Thr | missense_variant | 9/18 | ||
EXOC5 | XM_047430882.1 | c.572T>C | p.Ile191Thr | missense_variant | 9/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOC5 | ENST00000621441.5 | c.737T>C | p.Ile246Thr | missense_variant | 9/18 | 1 | NM_006544.4 | P1 | |
EXOC5 | ENST00000340918.11 | c.542T>C | p.Ile181Thr | missense_variant | 8/17 | 2 | |||
EXOC5 | ENST00000556629.1 | n.347T>C | non_coding_transcript_exon_variant | 4/6 | 3 | ||||
EXOC5 | ENST00000555148.5 | c.*571T>C | 3_prime_UTR_variant, NMD_transcript_variant | 9/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248334Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134702
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1458416Hom.: 0 Cov.: 28 AF XY: 0.0000110 AC XY: 8AN XY: 725712
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.737T>C (p.I246T) alteration is located in exon 9 (coding exon 9) of the EXOC5 gene. This alteration results from a T to C substitution at nucleotide position 737, causing the isoleucine (I) at amino acid position 246 to be replaced by a threonine (T). 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