chr5-55267707-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019030.4(DHX29):c.3410C>T(p.Thr1137Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,596,708 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. T1137K) has been classified as Uncertain significance.
Frequency
Consequence
NM_019030.4 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 |
---|---|---|---|---|---|---|---|
DHX29 | NM_019030.4 | c.3410C>T | p.Thr1137Met | missense_variant | 22/27 | ENST00000251636.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHX29 | ENST00000251636.10 | c.3410C>T | p.Thr1137Met | missense_variant | 22/27 | 1 | NM_019030.4 | P1 | |
DHX29 | ENST00000504778.5 | n.3618C>T | non_coding_transcript_exon_variant | 22/27 | 1 | ||||
CCNO-DT | ENST00000506435.1 | n.108-11826G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000667 AC: 10AN: 149912Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000935 AC: 23AN: 245972Hom.: 0 AF XY: 0.000128 AC XY: 17AN XY: 133082
GnomAD4 exome AF: 0.0000581 AC: 84AN: 1446678Hom.: 0 Cov.: 30 AF XY: 0.0000542 AC XY: 39AN XY: 719526
GnomAD4 genome ? AF: 0.0000667 AC: 10AN: 150030Hom.: 0 Cov.: 32 AF XY: 0.0000682 AC XY: 5AN XY: 73278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2022 | The c.3410C>T (p.T1137M) alteration is located in exon 22 (coding exon 22) of the DHX29 gene. This alteration results from a C to T substitution at nucleotide position 3410, causing the threonine (T) at amino acid position 1137 to be replaced by a methionine (M). 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