19-48834332-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016246.3(HSD17B14):c.154G>A(p.Glu52Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016246.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD17B14 | NM_016246.3 | c.154G>A | p.Glu52Lys | missense_variant | Exon 3 of 9 | ENST00000263278.9 | NP_057330.2 | |
HSD17B14 | XM_005258969.5 | c.154G>A | p.Glu52Lys | missense_variant | Exon 3 of 8 | XP_005259026.1 | ||
HSD17B14 | XM_047438897.1 | c.154G>A | p.Glu52Lys | missense_variant | Exon 3 of 7 | XP_047294853.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSD17B14 | ENST00000263278.9 | c.154G>A | p.Glu52Lys | missense_variant | Exon 3 of 9 | 1 | NM_016246.3 | ENSP00000263278.3 | ||
HSD17B14 | ENST00000599157.5 | c.154G>A | p.Glu52Lys | missense_variant | Exon 3 of 8 | 3 | ENSP00000472746.1 | |||
HSD17B14 | ENST00000595764.1 | c.46G>A | p.Glu16Lys | missense_variant | Exon 2 of 7 | 5 | ENSP00000469557.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251104Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135742
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461510Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727106
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.154G>A (p.E52K) alteration is located in exon 3 (coding exon 3) of the HSD17B14 gene. This alteration results from a G to A substitution at nucleotide position 154, causing the glutamic acid (E) at amino acid position 52 to be replaced by a lysine (K). 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