rs9264
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152233.4(SNX6):c.*159G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 683,520 control chromosomes in the GnomAD database, including 35,600 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 0.25 ( 6242 hom., cov: 33)
Exomes 𝑓: 0.32 ( 29358 hom. )
Consequence
SNX6
NM_152233.4 3_prime_UTR
NM_152233.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.170
Genes affected
SNX6 (HGNC:14970): (sorting nexin 6) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein associates with the long isoform of the leptin receptor, the transforming growth factor-beta family of receptor serine-threonine kinases, and with receptor tyrosine kinases for platelet-derived growth factor, insulin, and epidermal growth factor. This protein may form oligomeric complexes with family member proteins through interactions of both the PX domain and the coiled coil regions of the molecules. Translocation of this protein from the cytoplasm to the nucleus occurs after binding to proviral integration site 1 protein. This gene results in two transcripts encoding two distinct isoforms. [provided by RefSeq, Jul 2008]
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX6 | NM_152233.4 | c.*159G>A | 3_prime_UTR_variant | 14/14 | ENST00000362031.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX6 | ENST00000362031.10 | c.*159G>A | 3_prime_UTR_variant | 14/14 | 1 | NM_152233.4 | P1 | ||
SNX6 | ENST00000396526.7 | c.*159G>A | 3_prime_UTR_variant | 13/13 | 1 | ||||
SNX6 | ENST00000652385.1 | c.*159G>A | 3_prime_UTR_variant | 14/14 | |||||
SNX6 | ENST00000556162.6 | c.*1447G>A | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38658AN: 152094Hom.: 6241 Cov.: 33
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GnomAD4 exome AF: 0.320 AC: 170276AN: 531308Hom.: 29358 Cov.: 7 AF XY: 0.322 AC XY: 90142AN XY: 280210
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GnomAD4 genome ? AF: 0.254 AC: 38659AN: 152212Hom.: 6242 Cov.: 33 AF XY: 0.249 AC XY: 18536AN XY: 74408
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at