12-95878309-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_182496.3(CCDC38):āc.1180A>Gā(p.Met394Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000806 in 1,613,092 control chromosomes in the GnomAD database, including 2 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M394R) has been classified as Uncertain significance.
Frequency
Consequence
NM_182496.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC38 | NM_182496.3 | c.1180A>G | p.Met394Val | missense_variant | 13/16 | ENST00000344280.8 | |
CCDC38 | XM_011537883.3 | c.1180A>G | p.Met394Val | missense_variant | 13/16 | ||
CCDC38 | XM_047428281.1 | c.688A>G | p.Met230Val | missense_variant | 9/12 | ||
CCDC38 | XM_011537888.4 | c.529A>G | p.Met177Val | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC38 | ENST00000344280.8 | c.1180A>G | p.Met394Val | missense_variant | 13/16 | 1 | NM_182496.3 | P1 | |
SNRPF | ENST00000552085.1 | c.130-1379T>C | intron_variant | 3 | |||||
SNRPF | ENST00000553192.5 | c.130-1379T>C | intron_variant | 4 | |||||
CCDC38 | ENST00000549876.5 | c.67A>G | p.Met23Val | missense_variant, NMD_transcript_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000180 AC: 45AN: 250382Hom.: 1 AF XY: 0.000126 AC XY: 17AN XY: 135346
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1460894Hom.: 2 Cov.: 31 AF XY: 0.0000757 AC XY: 55AN XY: 726782
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.1180A>G (p.M394V) alteration is located in exon 13 (coding exon 12) of the CCDC38 gene. This alteration results from a A to G substitution at nucleotide position 1180, causing the methionine (M) at amino acid position 394 to be replaced by a valine (V). 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