6-85508320-T-TA

Variant summary

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

The NM_153816.6(SNX14):c.2654-262_2654-261insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0206 in 866,734 control chromosomes in the GnomAD database, including 128 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.034 (128 hom., cov: 31)
  • Exomes 𝑓: 0.019 (0 hom.)
• Consequence: SNX14 NM_153816.6 intron
• Clinical Significance: 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-T-TA is Benign according to our data. Variant chr6-85508320-T-TA is described in ClinVar as [Benign]. Clinvar id is 1246206.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX14	NM_153816.6	c.2654-262_2654-261insT		intron_variant		ENST00000314673.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX14	ENST00000314673.8	c.2654-262_2654-261insT		intron_variant		1	NM_153816.6	P4

Frequencies

GnomAD3 genomes AF: 0.0336 AC: 3331 AN: 98990 Hom.: 128 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00159

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.00458

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.0109

Gnomad NFE AF: 0.00335

Gnomad OTH AF: 0.0214

GnomAD4 exome AF: 0.0189 AC: 14548 AN: 767766 Hom.: 0 Cov.: 0 AF XY: 0.0185 AC XY: 6601 AN XY: 356654

Gnomad4 AFR exome AF: 0.0533

Gnomad4 AMR exome AF: 0.0172

Gnomad4 ASJ exome AF: 0.0142

Gnomad4 EAS exome AF: 0.0166

Gnomad4 SAS exome AF: 0.0184

Gnomad4 FIN exome AF: 0.0183

Gnomad4 NFE exome AF: 0.0183

Gnomad4 OTH exome AF: 0.0193

GnomAD4 genome AF: 0.0337 AC: 3331 AN: 98968 Hom.: 128 Cov.: 31 AF XY: 0.0328 AC XY: 1542 AN XY: 46974

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0151

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0142

Gnomad4 SAS AF: 0.00462

Gnomad4 FIN AF: 0.00189

Gnomad4 NFE AF: 0.00335

Gnomad4 OTH AF: 0.0214

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

Sep 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs765165360; hg19: chr6-86218038;