7-98217430-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_015395.3(TECPR1):​c.3458C>T​(p.Pro1153Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000673 in 1,607,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00089 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00065 ( 0 hom. )

Consequence

TECPR1
NM_015395.3 missense

Scores

2
17

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.97
Variant links:
Genes affected
TECPR1 (HGNC:22214): (tectonin beta-propeller repeat containing 1) This gene encodes a tethering factor involved in autophagy. The encoded protein is found at autolysosomes, and is involved in targeting protein aggregates, damaged mitochondria, and bacterial pathogens for autophagy [provided by RefSeq, Nov 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0076130033).
BP6
Variant 7-98217430-G-A is Benign according to our data. Variant chr7-98217430-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657695.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TECPR1NM_015395.3 linkc.3458C>T p.Pro1153Leu missense_variant 26/26 ENST00000447648.7 NP_056210.1 Q7Z6L1-1
TECPR1XM_005250253.5 linkc.3458C>T p.Pro1153Leu missense_variant 26/26 XP_005250310.1 Q7Z6L1-1
TECPR1XM_017011937.2 linkc.3356C>T p.Pro1119Leu missense_variant 25/25 XP_016867426.1
TECPR1XM_047420119.1 linkc.3356C>T p.Pro1119Leu missense_variant 25/25 XP_047276075.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TECPR1ENST00000447648.7 linkc.3458C>T p.Pro1153Leu missense_variant 26/261 NM_015395.3 ENSP00000404923.2 Q7Z6L1-1
TECPR1ENST00000490842.5 linkn.2656C>T non_coding_transcript_exon_variant 15/161
TECPR1ENST00000463402.5 linkn.970C>T non_coding_transcript_exon_variant 5/52
TECPR1ENST00000485716.1 linkn.221C>T non_coding_transcript_exon_variant 2/22

Frequencies

GnomAD3 genomes
AF:
0.000894
AC:
136
AN:
152180
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000217
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00347
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00104
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000882
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000776
AC:
185
AN:
238254
Hom.:
2
AF XY:
0.000889
AC XY:
116
AN XY:
130432
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00183
Gnomad ASJ exome
AF:
0.000313
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00120
Gnomad NFE exome
AF:
0.000824
Gnomad OTH exome
AF:
0.00138
GnomAD4 exome
AF:
0.000650
AC:
946
AN:
1455680
Hom.:
0
Cov.:
31
AF XY:
0.000681
AC XY:
493
AN XY:
723696
show subpopulations
Gnomad4 AFR exome
AF:
0.0000898
Gnomad4 AMR exome
AF:
0.00149
Gnomad4 ASJ exome
AF:
0.000194
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00107
Gnomad4 NFE exome
AF:
0.000691
Gnomad4 OTH exome
AF:
0.000682
GnomAD4 genome
AF:
0.000894
AC:
136
AN:
152180
Hom.:
0
Cov.:
33
AF XY:
0.00110
AC XY:
82
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.000217
Gnomad4 AMR
AF:
0.00347
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00104
Gnomad4 NFE
AF:
0.000882
Gnomad4 OTH
AF:
0.000956
Alfa
AF:
0.000447
Hom.:
0
Bravo
AF:
0.000835
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000483
AC:
4
ExAC
AF:
0.000465
AC:
56

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2023TECPR1: BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
-0.63
T
BayesDel_noAF
Benign
-0.69
CADD
Benign
6.0
DANN
Benign
0.96
DEOGEN2
Benign
0.019
T
Eigen
Benign
-0.91
Eigen_PC
Benign
-0.95
FATHMM_MKL
Benign
0.023
N
LIST_S2
Benign
0.58
T
M_CAP
Benign
0.0077
T
MetaRNN
Benign
0.0076
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L
PrimateAI
Benign
0.24
T
PROVEAN
Benign
-1.7
N
REVEL
Benign
0.037
Sift
Uncertain
0.011
D
Sift4G
Uncertain
0.018
D
Polyphen
0.10
B
Vest4
0.048
MVP
0.15
MPC
0.24
ClinPred
0.027
T
GERP RS
2.8
Varity_R
0.038
gMVP
0.30

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200095183; hg19: chr7-97846742; COSMIC: COSV58362908; COSMIC: COSV58362908; API