20-24629009-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SYNDIG1	NM_024893.3	c.619-36337A>G		intron_variant		ENST00000376862.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYNDIG1	ENST00000376862.4	c.619-36337A>G		intron_variant		1	NM_024893.3	P1

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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.610

Alfa AF: 0.613 Hom.: 56188

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

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: rs1883924; hg19: chr20-24609645;