4-181717360-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_017008385.2(TENM3):​c.-399-22127A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,966 control chromosomes in the GnomAD database, including 20,467 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 0.51 ( 20467 hom., cov: 32)

Consequence

TENM3
XM_017008385.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.386
Variant links:
Genes affected
TENM3 (HGNC:29944): (teneurin transmembrane protein 3) This gene encodes a member of the teneurin transmembrane protein family. The encoded protein may be involved in the regulation of neuronal development including development of the visual pathway. Mutations in this gene have been associated with microphthalmia and developmental dysplasia of the hip. [provided by RefSeq, Jan 2023]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TENM3XM_017008385.2 linkc.-399-22127A>G intron_variant XP_016863874.1
TENM3XM_047415933.1 linkc.-399-22127A>G intron_variant XP_047271889.1
TENM3XM_017008389.2 linkc.-399-22127A>G intron_variant XP_016863878.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.512
AC:
77673
AN:
151846
Hom.:
20452
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.373
Gnomad AMI
AF:
0.336
Gnomad AMR
AF:
0.622
Gnomad ASJ
AF:
0.501
Gnomad EAS
AF:
0.620
Gnomad SAS
AF:
0.515
Gnomad FIN
AF:
0.576
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.555
Gnomad OTH
AF:
0.538
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.511
AC:
77723
AN:
151966
Hom.:
20467
Cov.:
32
AF XY:
0.513
AC XY:
38153
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.373
Gnomad4 AMR
AF:
0.622
Gnomad4 ASJ
AF:
0.501
Gnomad4 EAS
AF:
0.619
Gnomad4 SAS
AF:
0.514
Gnomad4 FIN
AF:
0.576
Gnomad4 NFE
AF:
0.555
Gnomad4 OTH
AF:
0.539
Alfa
AF:
0.542
Hom.:
10590
Bravo
AF:
0.510
Asia WGS
AF:
0.549
AC:
1908
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
7.3
DANN
Benign
0.71

Splicing

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: rs6848193; hg19: chr4-182638513; API