6-85507730-G-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.2745+238C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,994 control chromosomes in the GnomAD database, including 42,580 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.74 (42580 hom., cov: 32)
• Consequence: SNX14 NM_153816.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.26

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=-0.92).
• BP6: Variant 6-85507730-G-T is Benign according to our data. Variant chr6-85507730-G-T is described in ClinVar as [Benign]. Clinvar id is 1272162.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX14	NM_153816.6	c.2745+238C>A		intron_variant		ENST00000314673.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX14	ENST00000314673.8	c.2745+238C>A		intron_variant		1	NM_153816.6	P4

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111831 AN: 151876 Hom.: 42515 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.737 AC: 111959 AN: 151994 Hom.: 42580 Cov.: 32 AF XY: 0.738 AC XY: 54764 AN XY: 74248

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.725

Alfa AF: 0.674 Hom.: 7132

Bravo AF: 0.758

Asia WGS AF: 0.726 AC: 2505 AN: 3452

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 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.42
Dann	Benign	0.21

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: rs4304137; hg19: chr6-86217448;