Genetic Variant NM_001284401.2:c.938-555C>T (chr3-11791136-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001284401.2(TAMM41):c.938-555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,204 control chromosomes in the GnomAD database, including 2,790 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 0.13 ( 2790 hom., cov: 33)

Consequence

TAMM41
NM_001284401.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130

Publications

2 publications found

Variant links:

Genes affected

TAMM41 (HGNC:25187): (TAM41 mitochondrial translocator assembly and maintenance homolog) Predicted to enable phosphatidate cytidylyltransferase activity. Predicted to be involved in CDP-diacylglycerol biosynthetic process and cardiolipin biosynthetic process. Predicted to be located in mitochondrial inner membrane. Predicted to be extrinsic component of mitochondrial inner membrane. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

TAMM41 Gene-Disease associations (from GenCC):

combined oxidative phosphorylation deficiency 56
Inheritance: AR Classification: STRONG, LIMITED Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)

TAMM41 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284401.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAMM41	NM_001284401.2	MANE Select	c.938-555C>T	intron	N/A	NP_001271330.1	Q96BW9-3
TAMM41	NM_138807.4		c.875-555C>T	intron	N/A	NP_620162.1	Q96BW9-2
TAMM41	NM_001321294.2		c.815-555C>T	intron	N/A	NP_001308223.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAMM41	ENST00000455809.6	TSL:3 MANE Select	c.938-555C>T	intron	N/A	ENSP00000398596.1	Q96BW9-3
TAMM41	ENST00000273037.9	TSL:1	c.875-555C>T	intron	N/A	ENSP00000273037.5	Q96BW9-2
TAMM41	ENST00000879036.1		c.944-555C>T	intron	N/A	ENSP00000549095.1

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19844

AN:

152086

Hom.:

2783

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.0642

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0168

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.131

AC:

19889

AN:

152204

Hom.:

2790

Cov.:

AF XY:

0.137

AC XY:

10165

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.302

AC:

12534

AN:

41510

American (AMR)

AF:

0.134

AC:

2044

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3472

East Asian (EAS)

AF:

0.482

AC:

2481

AN:

5148

South Asian (SAS)

AF:

0.148

AC:

712

AN:

4826

European-Finnish (FIN)

AF:

0.0642

AC:

681

AN:

10608

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0168

AC:

1146

AN:

68028

Other (OTH)

AF:

0.106

AC:

224

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

715

1431

2146

2862

3577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0738

Hom.:

180

Bravo

AF:

0.145

Asia WGS

AF:

0.275

AC:

955

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.1

(source)

DANN

Benign

0.46

PhyloP100

-0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over