chr14-102396422-A-G

Variant names:

• chr14-102396422-A-G
• rs4906195
• NM_014844.5:c.220-10916A>G

Variant summary

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

The NM_014844.5(TECPR2):​c.220-10916A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,068 control chromosomes in the GnomAD database, including 10,021 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 0.36 (10021 hom., cov: 31)
• Consequence: TECPR2 NM_014844.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 3 publications found

Genes affected

TECPR2 (HGNC:19957): (tectonin beta-propeller repeat containing 2) The protein encoded by this gene is a member of the tectonin beta-propeller repeat-containing (TECPR) family, and contains both TECPR and tryptophan-aspartic acid repeat (WD repeat) domains. This gene has been implicated in autophagy, as reduced expression levels of this gene have been associated with impaired autophagy. Recessive mutations in this gene have been associated with a hereditary form of spastic paraparesis (HSP). HSP is characterized by progressive spasticity and paralysis of the legs. There is also some evidence linking mutations in this gene with birdshot chorioretinopathy (BSCR), which results in inflammation of the choroid and retina. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

TECPR2 Gene-Disease associations (from GenCC):

• hereditary spastic paraplegia 49

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TECPR2	NM_014844.5	c.220-10916A>G		intron_variant	Intron 2 of 19	ENST00000359520.12	NP_055659.2
TECPR2	NM_001172631.3	c.220-10916A>G		intron_variant	Intron 2 of 16		NP_001166102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TECPR2	ENST00000359520.12	c.220-10916A>G		intron_variant	Intron 2 of 19	1	NM_014844.5	ENSP00000352510.7
TECPR2	ENST00000558678.1	c.220-10916A>G		intron_variant	Intron 2 of 16	1		ENSP00000453671.1
TECPR2	ENST00000561228.1	n.348-10916A>G		intron_variant	Intron 2 of 5	2

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54359 AN: 151950 Hom.: 10012 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.358 AC: 54401 AN: 152068 Hom.: 10021 Cov.: 31 AF XY: 0.351 AC XY: 26080 AN XY: 74340

African (AFR) AF: 0.322 AC: 13378 AN: 41484

American (AMR) AF: 0.324 AC: 4947 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1609 AN: 3466

East Asian (EAS) AF: 0.130 AC: 671 AN: 5168

South Asian (SAS) AF: 0.327 AC: 1575 AN: 4820

European-Finnish (FIN) AF: 0.289 AC: 3054 AN: 10578

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27953 AN: 67982

Other (OTH) AF: 0.379 AC: 799 AN: 2110

Alfa AF: 0.358 Hom.: 3967

Bravo AF: 0.355

Asia WGS AF: 0.259 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.3
DANN	Benign	0.81
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: rs4906195; hg19: chr14-102862759;