chr20-24635550-G-T

Variant names:

• chr20-24635550-G-T
• rs4815292
• NM_024893.3:c.619-29796G>T

Variant summary

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

The NM_024893.3(SYNDIG1):​c.619-29796G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,006 control chromosomes in the GnomAD database, including 18,986 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 0.46 (18986 hom., cov: 32)
• Consequence: SYNDIG1 NM_024893.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNDIG1	NM_024893.3	c.619-29796G>T		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.619-29796G>T		intron_variant	Intron 3 of 3	1	NM_024893.3	ENSP00000366058.3

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70283 AN: 151888 Hom.: 18972 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.463 AC: 70318 AN: 152006 Hom.: 18986 Cov.: 32 AF XY: 0.462 AC XY: 34326 AN XY: 74290

African (AFR) AF: 0.196 AC: 8136 AN: 41482

American (AMR) AF: 0.594 AC: 9077 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3470

East Asian (EAS) AF: 0.172 AC: 888 AN: 5172

South Asian (SAS) AF: 0.451 AC: 2169 AN: 4806

European-Finnish (FIN) AF: 0.571 AC: 6013 AN: 10538

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40624 AN: 67950

Other (OTH) AF: 0.464 AC: 976 AN: 2104

Alfa AF: 0.440 Hom.: 7063

Bravo AF: 0.453

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.82
PhyloP100		-0.20
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: rs4815292; hg19: chr20-24616186;