20-24635550-G-T

Position:

• chr20-24635550-G-T

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SYNDIG1	NM_024893.3	c.619-29796G>T		intron_variant		ENST00000376862.4	NP_079169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNDIG1	ENST00000376862.4	c.619-29796G>T		intron_variant		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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.464

Alfa AF: 0.543 Hom.: 3625

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

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: rs4815292; hg19: chr20-24616186;