chr14-105496322-G-T

Variant names:

• chr14-105496322-G-T
• rs7492357
• NM_001367178.1:c.891+236G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367178.1(TEDC1):​c.891+236G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
• Consequence: TEDC1 NM_001367178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 2 publications found

Genes affected

TEDC1 (HGNC:20127): (tubulin epsilon and delta complex 1) Predicted to be involved in positive regulation of smoothened signaling pathway. Predicted to be located in centriole and cilium. [provided by Alliance of Genome Resources, Apr 2022]

TEDC1 Gene-Disease associations (from GenCC):

• autosomal recessive primary microcephaly

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
• microcephaly

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEDC1	NM_001367178.1	MANE Select	c.891+236G>T		intron	N/A	NP_001354107.1
	TEDC1	NM_001134875.2		c.685-1035G>T		intron	N/A	NP_001128347.1
	TEDC1	NM_001134876.2		c.586-1035G>T		intron	N/A	NP_001128348.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEDC1	ENST00000392523.9	TSL:1 MANE Select	c.891+236G>T		intron	N/A	ENSP00000376308.4
	TEDC1	ENST00000354560.10	TSL:1	c.586-1035G>T		intron	N/A	ENSP00000346568.6
	TEDC1	ENST00000329886.11	TSL:1	c.469-1035G>T		intron	N/A	ENSP00000333010.7

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Cov.: 4

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.92
PhyloP100		1.0

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: rs7492357; hg19: chr14-105962659;