2-143947122-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001376312.2(GTDC1):c.1307C>T(p.Pro436Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000701 in 1,613,222 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001376312.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GTDC1 | NM_001376312.2 | c.1307C>T | p.Pro436Leu | missense_variant | 12/12 | ENST00000682281.1 | NP_001363241.1 | |
LOC101928386 | NR_110237.1 | n.721+5958G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTDC1 | ENST00000682281.1 | c.1307C>T | p.Pro436Leu | missense_variant | 12/12 | NM_001376312.2 | ENSP00000507713 | P1 | ||
ENST00000422799.1 | n.715+5958G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000703 AC: 107AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000916 AC: 229AN: 250012Hom.: 3 AF XY: 0.00109 AC XY: 147AN XY: 135260
GnomAD4 exome AF: 0.000701 AC: 1024AN: 1460974Hom.: 8 Cov.: 29 AF XY: 0.000828 AC XY: 602AN XY: 726890
GnomAD4 genome AF: 0.000703 AC: 107AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at