chr16-10941969-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014015.4(DEXI):c.37C>G(p.Leu13Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,529,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014015.4 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 | UniProt |
---|---|---|---|---|---|---|---|
DEXI | NM_014015.4 | c.37C>G | p.Leu13Val | missense_variant | 1/2 | ENST00000331808.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEXI | ENST00000331808.5 | c.37C>G | p.Leu13Val | missense_variant | 1/2 | 1 | NM_014015.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000723 AC: 10AN: 138390Hom.: 0 AF XY: 0.0000531 AC XY: 4AN XY: 75334
GnomAD4 exome AF: 0.0000820 AC: 113AN: 1377306Hom.: 0 Cov.: 30 AF XY: 0.0000676 AC XY: 46AN XY: 680186
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2023 | The c.37C>G (p.L13V) alteration is located in exon 1 (coding exon 1) of the DEXI gene. This alteration results from a C to G substitution at nucleotide position 37, causing the leucine (L) at amino acid position 13 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