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chr16-28842675-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003321.5(TUFM):​c.*300T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 438,128 control chromosomes in the GnomAD database, including 27,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 9551 hom., cov: 32)
Exomes 𝑓: 0.34 ( 18289 hom. )

Consequence

TUFM
NM_003321.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.57
Variant links:
Genes affected
TUFM (HGNC:12420): (Tu translation elongation factor, mitochondrial) This gene encodes a protein which participates in protein translation in mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency resulting in lactic acidosis and fatal encephalopathy. A pseudogene has been identified on chromosome 17. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 16-28842675-A-C is Benign according to our data. Variant chr16-28842675-A-C is described in ClinVar as [Benign]. Clinvar id is 318738.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TUFMNM_003321.5 linkuse as main transcriptc.*300T>G 3_prime_UTR_variant 10/10 ENST00000313511.8
TUFMNM_001365360.2 linkuse as main transcriptc.*300T>G 3_prime_UTR_variant 10/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TUFMENST00000313511.8 linkuse as main transcriptc.*300T>G 3_prime_UTR_variant 10/101 NM_003321.5 P1

Frequencies

GnomAD3 genomes
AF:
0.341
AC:
51873
AN:
151980
Hom.:
9522
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.266
Gnomad AMI
AF:
0.246
Gnomad AMR
AF:
0.405
Gnomad ASJ
AF:
0.267
Gnomad EAS
AF:
0.122
Gnomad SAS
AF:
0.217
Gnomad FIN
AF:
0.423
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.393
Gnomad OTH
AF:
0.305
GnomAD4 exome
AF:
0.344
AC:
98372
AN:
286030
Hom.:
18289
Cov.:
0
AF XY:
0.333
AC XY:
50768
AN XY:
152444
show subpopulations
Gnomad4 AFR exome
AF:
0.261
Gnomad4 AMR exome
AF:
0.452
Gnomad4 ASJ exome
AF:
0.270
Gnomad4 EAS exome
AF:
0.122
Gnomad4 SAS exome
AF:
0.225
Gnomad4 FIN exome
AF:
0.420
Gnomad4 NFE exome
AF:
0.389
Gnomad4 OTH exome
AF:
0.343
GnomAD4 genome
AF:
0.342
AC:
51966
AN:
152098
Hom.:
9551
Cov.:
32
AF XY:
0.340
AC XY:
25258
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.267
Gnomad4 AMR
AF:
0.406
Gnomad4 ASJ
AF:
0.267
Gnomad4 EAS
AF:
0.121
Gnomad4 SAS
AF:
0.217
Gnomad4 FIN
AF:
0.423
Gnomad4 NFE
AF:
0.393
Gnomad4 OTH
AF:
0.309
Alfa
AF:
0.377
Hom.:
1437
Bravo
AF:
0.339
Asia WGS
AF:
0.275
AC:
952
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Combined oxidative phosphorylation defect type 4 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. -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.83
DANN
Benign
0.67

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: rs3088215; hg19: chr16-28853996; API