chr6-85505762-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_153816.6(SNX14):c.*205C>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 0.00291 in 528,902 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0078 ( 12 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 5 hom. )
Consequence
SNX14
NM_153816.6 3_prime_UTR
NM_153816.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.254
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 6-85505762-G-A is Benign according to our data. Variant chr6-85505762-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1205055.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00777 (1182/152062) while in subpopulation AFR AF= 0.0267 (1108/41474). AF 95% confidence interval is 0.0254. There are 12 homozygotes in gnomad4. There are 561 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX14 | NM_153816.6 | c.*205C>T | 3_prime_UTR_variant | 29/29 | ENST00000314673.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX14 | ENST00000314673.8 | c.*205C>T | 3_prime_UTR_variant | 29/29 | 1 | NM_153816.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00779 AC: 1183AN: 151944Hom.: 12 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1183
AN:
151944
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000953 AC: 359AN: 376840Hom.: 5 Cov.: 3 AF XY: 0.000765 AC XY: 155AN XY: 202540
GnomAD4 exome
AF:
AC:
359
AN:
376840
Hom.:
Cov.:
3
AF XY:
AC XY:
155
AN XY:
202540
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00777 AC: 1182AN: 152062Hom.: 12 Cov.: 32 AF XY: 0.00755 AC XY: 561AN XY: 74336
GnomAD4 genome
?
AF:
AC:
1182
AN:
152062
Hom.:
Cov.:
32
AF XY:
AC XY:
561
AN XY:
74336
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3
AN:
3470
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 | Jan 12, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at