chr14-81312300-G-A

Variant names:

• chr14-81312300-G-A
• rs6574644
• NM_001394390.1:c.742+11717C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394390.1(STON2):​c.742+11717C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,024 control chromosomes in the GnomAD database, including 47,255 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (47255 hom., cov: 30)
• Consequence: STON2 NM_001394390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 8 publications found

Genes affected

STON2 (HGNC:30652): (stonin 2) This gene encodes a protein which is a membrane protein involved in regulating endocytotic complexes. The protein product is described as one of the clathrin-associated sorting proteins, adaptor molecules which ensure specific proteins are internalized. The encoded protein has also been shown to participate in synaptic vesicle recycling through interaction with synaptotagmin 1 required for neurotransmission. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STON2	NM_001394390.1	c.742+11717C>T		intron_variant	Intron 5 of 7	ENST00000614646.5	NP_001381319.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STON2	ENST00000614646.5	c.742+11717C>T		intron_variant	Intron 5 of 7	5	NM_001394390.1	ENSP00000477736.2

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119588 AN: 151906 Hom.: 47217 Cov.: 30

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.787 AC: 119676 AN: 152024 Hom.: 47255 Cov.: 30 AF XY: 0.786 AC XY: 58411 AN XY: 74310

African (AFR) AF: 0.800 AC: 33137 AN: 41430

American (AMR) AF: 0.763 AC: 11652 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2880 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3177 AN: 5156

South Asian (SAS) AF: 0.753 AC: 3628 AN: 4816

European-Finnish (FIN) AF: 0.805 AC: 8526 AN: 10590

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53901 AN: 67972

Other (OTH) AF: 0.810 AC: 1706 AN: 2106

Alfa AF: 0.793 Hom.: 192480

Bravo AF: 0.788

Asia WGS AF: 0.642 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.48
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6574644; hg19: chr14-81778644;