chr6-85507915-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_153816.6(SNX14):c.2745+53G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00237 in 1,419,042 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 28 hom., cov: 31)
Exomes 𝑓: 0.0013 ( 26 hom. )
Consequence
SNX14
NM_153816.6 intron
NM_153816.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.243
Genes affected
SNX14 (HGNC:14977): (sorting nexin 14) This gene encodes a member of the sorting nexin family. Members of this family have a phox (PX) phosphoinositide binding domain and are involved in intracellular trafficking. The encoded protein also contains a regulator of G protein signaling (RGS) domain. Regulator of G protein signaling family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. Alternate splicing results in transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 6-85507915-C-T is Benign according to our data. Variant chr6-85507915-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1208139.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0112 (1708/152190) while in subpopulation AFR AF= 0.0384 (1594/41502). AF 95% confidence interval is 0.0368. There are 28 homozygotes in gnomad4. There are 826 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 28 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX14 | NM_153816.6 | c.2745+53G>A | intron_variant | ENST00000314673.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX14 | ENST00000314673.8 | c.2745+53G>A | intron_variant | 1 | NM_153816.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0112 AC: 1707AN: 152072Hom.: 28 Cov.: 31
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GnomAD4 exome AF: 0.00131 AC: 1658AN: 1266852Hom.: 26 AF XY: 0.00110 AC XY: 704AN XY: 639768
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GnomAD4 genome ? AF: 0.0112 AC: 1708AN: 152190Hom.: 28 Cov.: 31 AF XY: 0.0111 AC XY: 826AN XY: 74410
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at