6-85508320-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_153816.6(SNX14):c.2654-262del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0070 (2 hom., cov: 31)
  • Exomes 𝑓: 0.30 (4 hom.)
  • Failed GnomAD Quality Control
• Consequence: SNX14 NM_153816.6 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.381

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 -10 ACMG points.

• BP6: Variant 6-85508320-TA-T is Benign according to our data. Variant chr6-85508320-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1206587.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX14	NM_153816.6	c.2654-262del		intron_variant		ENST00000314673.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX14	ENST00000314673.8	c.2654-262del		intron_variant		1	NM_153816.6	P4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 686 AN: 98994 Hom.: 2 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00864

Gnomad ASJ AF: 0.00166

Gnomad EAS AF: 0.00393

Gnomad SAS AF: 0.00275

Gnomad FIN AF: 0.0158

Gnomad MID AF: 0.00543

Gnomad NFE AF: 0.00326

Gnomad OTH AF: 0.00740

GnomAD4 exome AF: 0.299 AC: 221523 AN: 740090 Hom.: 4 Cov.: 0 AF XY: 0.299 AC XY: 102884 AN XY: 343578

Gnomad4 AFR exome AF: 0.285

Gnomad4 AMR exome AF: 0.258

Gnomad4 ASJ exome AF: 0.288

Gnomad4 EAS exome AF: 0.270

Gnomad4 SAS exome AF: 0.293

Gnomad4 FIN exome AF: 0.213

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.302

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00695 AC: 688 AN: 98972 Hom.: 2 Cov.: 31 AF XY: 0.00762 AC XY: 358 AN XY: 46978

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.00875

Gnomad4 ASJ AF: 0.00166

Gnomad4 EAS AF: 0.00394

Gnomad4 SAS AF: 0.00246

Gnomad4 FIN AF: 0.0158

Gnomad4 NFE AF: 0.00326

Gnomad4 OTH AF: 0.00737

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs765165360; hg19: chr6-86218038;