chr5-118939274-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173666.4(DTWD2):c.326G>A(p.Arg109His) variant causes a missense change. The variant allele was found at a frequency of 0.0000973 in 1,583,246 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. R109C) has been classified as Uncertain significance.
Frequency
Consequence
NM_173666.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTWD2 | NM_173666.4 | c.326G>A | p.Arg109His | missense_variant | 3/6 | ENST00000510708.6 | |
DTWD2 | NM_001308081.2 | c.128G>A | p.Arg43His | missense_variant | 3/6 | ||
DTWD2 | XM_011543338.4 | c.326G>A | p.Arg109His | missense_variant | 3/7 | ||
DTWD2 | XM_011543340.3 | c.128G>A | p.Arg43His | missense_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTWD2 | ENST00000510708.6 | c.326G>A | p.Arg109His | missense_variant | 3/6 | 1 | NM_173666.4 | P1 | |
DTWD2 | ENST00000304058.8 | c.128G>A | p.Arg43His | missense_variant | 3/6 | 1 | |||
DTWD2 | ENST00000515439.7 | c.309+5285G>A | intron_variant | 5 | |||||
DTWD2 | ENST00000506980.2 | c.326G>A | p.Arg109His | missense_variant, NMD_transcript_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000768 AC: 18AN: 234276Hom.: 0 AF XY: 0.0000709 AC XY: 9AN XY: 127028
GnomAD4 exome AF: 0.0000978 AC: 140AN: 1431022Hom.: 0 Cov.: 30 AF XY: 0.000104 AC XY: 74AN XY: 711600
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.326G>A (p.R109H) alteration is located in exon 3 (coding exon 3) of the DTWD2 gene. This alteration results from a G to A substitution at nucleotide position 326, causing the arginine (R) at amino acid position 109 to be replaced by a histidine (H). 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