rs464218
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002959.7(SORT1):c.*359C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 276,184 control chromosomes in the GnomAD database, including 34,608 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 16567 hom., cov: 33)
Exomes 𝑓: 0.53 ( 18041 hom. )
Consequence
SORT1
NM_002959.7 3_prime_UTR
NM_002959.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.690
Genes affected
SORT1 (HGNC:11186): (sortilin 1) This gene encodes a member of the VPS10-related sortilin family of proteins. The encoded preproprotein is proteolytically processed by furin to generate the mature receptor. This receptor plays a role in the trafficking of different proteins to either the cell surface, or subcellular compartments such as lysosomes and endosomes. Expression levels of this gene may influence the risk of myocardial infarction in human patients. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SORT1 | NM_002959.7 | c.*359C>T | 3_prime_UTR_variant | 20/20 | ENST00000256637.8 | ||
SORT1 | NM_001205228.2 | c.*359C>T | 3_prime_UTR_variant | 20/20 | |||
SORT1 | XM_005271100.3 | c.*359C>T | 3_prime_UTR_variant | 20/20 | |||
SORT1 | XM_005271101.4 | c.*359C>T | 3_prime_UTR_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SORT1 | ENST00000256637.8 | c.*359C>T | 3_prime_UTR_variant | 20/20 | 1 | NM_002959.7 | P1 | ||
SORT1 | ENST00000538502.5 | c.*359C>T | 3_prime_UTR_variant | 20/20 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.436 AC: 66245AN: 152040Hom.: 16558 Cov.: 33
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GnomAD4 exome AF: 0.527 AC: 65367AN: 124026Hom.: 18041 Cov.: 0 AF XY: 0.524 AC XY: 34443AN XY: 65682
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GnomAD4 genome ? AF: 0.436 AC: 66267AN: 152158Hom.: 16567 Cov.: 33 AF XY: 0.437 AC XY: 32536AN XY: 74392
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at