16-75529700-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_024533.5(CHST5):c.685G>A(p.Val229Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00091 in 1,610,994 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024533.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST5 | ENST00000336257.8 | c.685G>A | p.Val229Met | missense_variant | Exon 4 of 4 | 1 | NM_024533.5 | ENSP00000338783.3 | ||
ENSG00000260092 | ENST00000460606.1 | n.*784G>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 | ENSP00000457544.1 | ||||
ENSG00000260092 | ENST00000460606.1 | n.*784G>A | 3_prime_UTR_variant | Exon 5 of 5 | 1 | ENSP00000457544.1 |
Frequencies
GnomAD3 genomes AF: 0.000710 AC: 108AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000438 AC: 106AN: 242096Hom.: 0 AF XY: 0.000417 AC XY: 55AN XY: 131804
GnomAD4 exome AF: 0.000931 AC: 1358AN: 1458728Hom.: 2 Cov.: 34 AF XY: 0.000885 AC XY: 642AN XY: 725610
GnomAD4 genome AF: 0.000709 AC: 108AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000483 AC XY: 36AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.685G>A (p.V229M) alteration is located in exon 3 (coding exon 1) of the CHST5 gene. This alteration results from a G to A substitution at nucleotide position 685, causing the valine (V) at amino acid position 229 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