20-58652371-A-AC

Position:

• chr20-58652371-A-AC

Variant summary

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

The NM_001001433.3(STX16):​c.132+244dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 455,454 control chromosomes in the GnomAD database, including 3,296 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.26 (3250 hom., cov: 0)
  • Exomes 𝑓: 0.21 (46 hom.)
• Consequence: STX16 NM_001001433.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.774

Genes affected

STX16 (HGNC:11431): (syntaxin 16) This gene encodes a protein that is a member of the syntaxin or t-SNARE (target-SNAP receptor) family. These proteins are found on cell membranes and serve as the targets for V-SNARES (vesicle-SNAP receptors) permitting specific synaptic vesicle docking and fusion. A microdeletion in the region of chromosome 20 where this gene is located has been associated with pseudohypoparathyroidism type Ib. Multiple transcript variants have been found for this gene. Read-through transcription also exists between this gene and the neighboring downstream aminopeptidase-like 1 (NPEPL1) gene. [provided by RefSeq, Mar 2011]

STX16-NPEPL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 20-58652371-A-AC is Benign according to our data. Variant chr20-58652371-A-AC is described in ClinVar as [Benign]. Clinvar id is 1283105.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX16	NM_001001433.3	c.132+244dup		intron_variant		ENST00000371141.8
STX16-NPEPL1	NR_037945.1	n.886+244dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX16	ENST00000371141.8	c.132+244dup		intron_variant		2	NM_001001433.3	P3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 26388 AN: 102208 Hom.: 3253 Cov.: 0

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.258

GnomAD4 exome AF: 0.213 AC: 75284 AN: 353200 Hom.: 46 AF XY: 0.214 AC XY: 41490 AN XY: 193970

Gnomad4 AFR exome AF: 0.148

Gnomad4 AMR exome AF: 0.255

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.207

Gnomad4 SAS exome AF: 0.229

Gnomad4 FIN exome AF: 0.237

Gnomad4 NFE exome AF: 0.210

Gnomad4 OTH exome AF: 0.210

GnomAD4 genome AF: 0.258 AC: 26376 AN: 102254 Hom.: 3250 Cov.: 0 AF XY: 0.256 AC XY: 12320 AN XY: 48174

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.256

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

May 26, 2021

- -

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: rs11481928; hg19: chr20-57227427;