20-24629009-A-G

Variant names:

• chr20-24629009-A-G
• rs1883924
• NM_024893.3:c.619-36337A>G

Variant summary

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

The NM_024893.3(SYNDIG1):​c.619-36337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,160 control chromosomes in the GnomAD database, including 27,965 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 0.60 (27965 hom., cov: 33)
• Consequence: SYNDIG1 NM_024893.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 2 publications found

Genes affected

SYNDIG1 (HGNC:15885): (synapse differentiation inducing 1) This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]

SYNDIG1 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNDIG1	NM_024893.3	c.619-36337A>G		intron_variant	Intron 3 of 3	ENST00000376862.4	NP_079169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYNDIG1	ENST00000376862.4	c.619-36337A>G		intron_variant	Intron 3 of 3	1	NM_024893.3	ENSP00000366058.3

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91838 AN: 152040 Hom.: 27921 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.604 AC: 91936 AN: 152160 Hom.: 27965 Cov.: 33 AF XY: 0.606 AC XY: 45088 AN XY: 74388

African (AFR) AF: 0.542 AC: 22482 AN: 41502

American (AMR) AF: 0.663 AC: 10132 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2132 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3248 AN: 5168

South Asian (SAS) AF: 0.562 AC: 2711 AN: 4826

European-Finnish (FIN) AF: 0.651 AC: 6904 AN: 10606

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42464 AN: 67980

Other (OTH) AF: 0.610 AC: 1288 AN: 2112

Alfa AF: 0.614 Hom.: 121291

Bravo AF: 0.603

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.41
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: rs1883924; hg19: chr20-24609645;