6-85506179-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_153816.6(SNX14):c.2803-174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,070 control chromosomes in the GnomAD database, including 828 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.082 (828 hom., cov: 32)
• Consequence: SNX14 NM_153816.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.314

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 6-85506179-C-T is Benign according to our data. Variant chr6-85506179-C-T is described in ClinVar as [Benign]. Clinvar id is 1276013.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX14	NM_153816.6	c.2803-174G>A		intron_variant		ENST00000314673.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX14	ENST00000314673.8	c.2803-174G>A		intron_variant		1	NM_153816.6	P4

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12441 AN: 151952 Hom.: 830 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0305

Gnomad OTH AF: 0.0917

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0819 AC: 12449 AN: 152070 Hom.: 828 Cov.: 32 AF XY: 0.0854 AC XY: 6347 AN XY: 74334

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0305

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0472 Hom.: 59

Bravo AF: 0.0893

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13198956; hg19: chr6-86215897;