GeneBe

6-85508320-TAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_153816.6(SNX14):​c.2654-262_2654-261insTTTTTTTTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

SNX14
NM_153816.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.381
Variant links:
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX14NM_153816.6 linkc.2654-262_2654-261insTTTTTTTTTTTTTTTTTTTTTTTT intron_variant Intron 26 of 28 ENST00000314673.8 NP_722523.1 Q9Y5W7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNX14ENST00000314673.8 linkc.2654-262_2654-261insTTTTTTTTTTTTTTTTTTTTTTTT intron_variant Intron 26 of 28 1 NM_153816.6 ENSP00000313121.3 Q9Y5W7-1
ENSG00000271793ENST00000682083.1 linkn.*2564-262_*2564-261insTTTTTTTTTTTTTTTTTTTTTTTT intron_variant Intron 37 of 39 ENSP00000506859.1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs765165360; hg19: chr6-86218038; API