3-11791136-G-A

Variant names:

• chr3-11791136-G-A
• rs10510406
• NM_001284401.2:c.938-555C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 2 publications found

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: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAMM41	NM_001284401.2	c.938-555C>T		intron_variant	Intron 7 of 7	ENST00000455809.6	NP_001271330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAMM41	ENST00000455809.6	c.938-555C>T		intron_variant	Intron 7 of 7	3	NM_001284401.2	ENSP00000398596.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19844 AN: 152086 Hom.: 2783 Cov.: 33

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.: 33 AF XY: 0.137 AC XY: 10165 AN XY: 74398

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: 52 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: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0168 AC: 1146 AN: 68028

Other (OTH) AF: 0.106 AC: 224 AN: 2114

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10510406; hg19: chr3-11832610;