12-104457405-C-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_018413.6(CHST11):c.-7C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00484 in 1,609,418 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_018413.6 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.-7C>A | 5_prime_UTR_variant | Exon 1 of 3 | ENST00000303694.6 | NP_060883.1 | ||
CHST11 | NM_001173982.2 | c.-7C>A | 5_prime_UTR_variant | Exon 1 of 3 | NP_001167453.1 | |||
CHST11 | XM_047428914.1 | c.-158C>A | 5_prime_UTR_variant | Exon 1 of 2 | XP_047284870.1 | |||
CHST11 | XM_047428915.1 | c.-143C>A | 5_prime_UTR_variant | Exon 1 of 2 | XP_047284871.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST11 | ENST00000303694 | c.-7C>A | 5_prime_UTR_variant | Exon 1 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | |||
CHST11 | ENST00000549260 | c.-7C>A | 5_prime_UTR_variant | Exon 1 of 3 | 1 | ENSP00000450004.1 | ||||
CHST11 | ENST00000547956 | c.-7C>A | 5_prime_UTR_variant | Exon 1 of 2 | 2 | ENSP00000449093.1 | ||||
CHST11 | ENST00000546689 | c.-7C>A | 5_prime_UTR_variant | Exon 1 of 2 | 2 | ENSP00000448678.1 |
Frequencies
GnomAD3 genomes AF: 0.00282 AC: 429AN: 152210Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00238 AC: 595AN: 249862Hom.: 0 AF XY: 0.00246 AC XY: 333AN XY: 135224
GnomAD4 exome AF: 0.00505 AC: 7365AN: 1457092Hom.: 33 Cov.: 29 AF XY: 0.00483 AC XY: 3504AN XY: 725214
GnomAD4 genome AF: 0.00282 AC: 429AN: 152326Hom.: 1 Cov.: 32 AF XY: 0.00246 AC XY: 183AN XY: 74508
ClinVar
Submissions by phenotype
CHST11-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at