3-16175422-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_054110.5(GALNT15):c.271C>T(p.Arg91Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000069 ( 0 hom. )
Consequence
GALNT15
NM_054110.5 missense
NM_054110.5 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 0.0440
Genes affected
GALNT15 (HGNC:21531): (polypeptide N-acetylgalactosaminyltransferase 15) Predicted to enable polypeptide N-acetylgalactosaminyltransferase activity. Predicted to be involved in O-glycan processing. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23361537).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT15 | NM_054110.5 | c.271C>T | p.Arg91Trp | missense_variant | 1/10 | ENST00000339732.10 | NP_473451.3 | |
GALNT15 | NM_001319051.2 | c.271C>T | p.Arg91Trp | missense_variant | 1/10 | NP_001305980.1 | ||
GALNT15 | XM_005264852.6 | c.271C>T | p.Arg91Trp | missense_variant | 1/10 | XP_005264909.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT15 | ENST00000339732.10 | c.271C>T | p.Arg91Trp | missense_variant | 1/10 | 1 | NM_054110.5 | ENSP00000344260.5 | ||
GALNT15 | ENST00000437509.3 | c.271C>T | p.Arg91Trp | missense_variant | 1/10 | 1 | ENSP00000395873.1 | |||
GALNT15 | ENST00000470031.1 | n.6C>T | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251362Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135868
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GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000701 AC XY: 51AN XY: 727242
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74298
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 21, 2024 | The c.271C>T (p.R91W) alteration is located in exon 1 (coding exon 1) of the GALNT15 gene. This alteration results from a C to T substitution at nucleotide position 271, causing the arginine (R) at amino acid position 91 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at