18-12329456-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_006796.3(AFG3L2):​c.*109A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00199 in 1,177,410 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0084 ( 21 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 14 hom. )

Consequence

AFG3L2
NM_006796.3 3_prime_UTR

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.922
Variant links:
Genes affected
AFG3L2 (HGNC:315): (AFG3 like matrix AAA peptidase subunit 2) This gene encodes a protein localized in mitochondria and closely related to paraplegin. The paraplegin gene is responsible for an autosomal recessive form of hereditary spastic paraplegia. This gene is a candidate gene for other hereditary spastic paraplegias or neurodegenerative disorders. [provided by RefSeq, Jul 2008]
TUBB6 (HGNC:20776): (tubulin beta 6 class V) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Located in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 18-12329456-T-G is Benign according to our data. Variant chr18-12329456-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 326100.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00842 (1283/152356) while in subpopulation AFR AF= 0.0293 (1219/41584). AF 95% confidence interval is 0.0279. There are 21 homozygotes in gnomad4. There are 607 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 21 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AFG3L2NM_006796.3 linkuse as main transcriptc.*109A>C 3_prime_UTR_variant 17/17 ENST00000269143.8 NP_006787.2
TUBB6NM_001303525.2 linkuse as main transcriptc.*273T>G 3_prime_UTR_variant 4/4 NP_001290454.1
AFG3L2XM_011525601.4 linkuse as main transcriptc.*109A>C 3_prime_UTR_variant 16/16 XP_011523903.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AFG3L2ENST00000269143.8 linkuse as main transcriptc.*109A>C 3_prime_UTR_variant 17/171 NM_006796.3 ENSP00000269143 P1

Frequencies

GnomAD3 genomes
AF:
0.00841
AC:
1280
AN:
152238
Hom.:
20
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0293
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00621
GnomAD4 exome
AF:
0.00104
AC:
1062
AN:
1025054
Hom.:
14
Cov.:
14
AF XY:
0.000890
AC XY:
471
AN XY:
529152
show subpopulations
Gnomad4 AFR exome
AF:
0.0315
Gnomad4 AMR exome
AF:
0.00158
Gnomad4 ASJ exome
AF:
0.0000858
Gnomad4 EAS exome
AF:
0.0000266
Gnomad4 SAS exome
AF:
0.000143
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000138
Gnomad4 OTH exome
AF:
0.00202
GnomAD4 genome
AF:
0.00842
AC:
1283
AN:
152356
Hom.:
21
Cov.:
33
AF XY:
0.00815
AC XY:
607
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.0293
Gnomad4 AMR
AF:
0.00261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00615
Alfa
AF:
0.00707
Hom.:
3
Bravo
AF:
0.00963
Asia WGS
AF:
0.00202
AC:
7
AN:
3478

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Likely benign, criteria provided, single submitterclinical testingGeneDxDec 17, 2018- -
Spinocerebellar ataxia type 28 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
3.1
DANN
Benign
0.77

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: rs114203162; hg19: chr18-12329455; API