14-24440249-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020195.3(SDR39U1):c.716G>A(p.Arg239Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000242 in 1,613,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020195.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDR39U1 | ENST00000399395.8 | c.716G>A | p.Arg239Gln | missense_variant | Exon 6 of 6 | 1 | NM_020195.3 | ENSP00000382327.3 | ||
KHNYN | ENST00000553935.6 | c.*2964C>T | 3_prime_UTR_variant | Exon 8 of 8 | 1 | NM_015299.3 | ENSP00000450799.1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152212Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000406 AC: 10AN: 246476Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133956
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461542Hom.: 0 Cov.: 68 AF XY: 0.0000220 AC XY: 16AN XY: 727030
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152212Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.716G>A (p.R239Q) alteration is located in exon 6 (coding exon 6) of the SDR39U1 gene. This alteration results from a G to A substitution at nucleotide position 716, causing the arginine (R) at amino acid position 239 to be replaced by a glutamine (Q). 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