chr20-24648435-G-T

Position:

• chr20-24648435-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.619-16911G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,250 control chromosomes in the GnomAD database, including 3,558 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 0.20 (3558 hom., cov: 33)
• Consequence: SYNDIG1 NM_024893.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYNDIG1	NM_024893.3	c.619-16911G>T		intron_variant		ENST00000376862.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYNDIG1	ENST00000376862.4	c.619-16911G>T		intron_variant		1	NM_024893.3	P1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29687 AN: 152132 Hom.: 3556 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.195 AC: 29691 AN: 152250 Hom.: 3558 Cov.: 33 AF XY: 0.197 AC XY: 14631 AN XY: 74432

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.223

Alfa AF: 0.215 Hom.: 3648

Bravo AF: 0.192

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.37

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: rs11696125; hg19: chr20-24629071;