19-48939551-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014475.4(DHDH):c.469A>T(p.Asn157Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_014475.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHDH | NM_014475.4 | c.469A>T | p.Asn157Tyr | missense_variant | 4/7 | ENST00000221403.7 | |
DHDH | XM_017026598.2 | c.220A>T | p.Asn74Tyr | missense_variant | 4/7 | ||
DHDH | XM_047438617.1 | c.469A>T | p.Asn157Tyr | missense_variant | 4/5 | ||
DHDH | XM_005258748.5 | c.133A>T | p.Asn45Tyr | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHDH | ENST00000221403.7 | c.469A>T | p.Asn157Tyr | missense_variant | 4/7 | 1 | NM_014475.4 | P1 | |
DHDH | ENST00000522614.5 | c.469A>T | p.Asn157Tyr | missense_variant | 4/5 | 5 | |||
DHDH | ENST00000523250.5 | c.203-2889A>T | intron_variant | 5 | |||||
DHDH | ENST00000520557.1 | c.269A>T | p.Glu90Val | missense_variant, NMD_transcript_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727242
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.469A>T (p.N157Y) alteration is located in exon 4 (coding exon 4) of the DHDH gene. This alteration results from a A to T substitution at nucleotide position 469, causing the asparagine (N) at amino acid position 157 to be replaced by a tyrosine (Y). 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