rs6971

chr22-43162920-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000714.6(TSPO):c.439A>G(p.Thr147Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.712 in 1,593,126 control chromosomes in the GnomAD database, including 408,706 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.75 (43147 hom., cov: 35)
  • Exomes 𝑓: 0.71 (365559 hom.)
• Consequence: TSPO NM_000714.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.42

Genes affected

TSPO (HGNC:1158): (translocator protein) Present mainly in the mitochondrial compartment of peripheral tissues, the protein encoded by this gene interacts with some benzodiazepines and has different affinities than its endogenous counterpart. The protein is a key factor in the flow of cholesterol into mitochondria to permit the initiation of steroid hormone synthesis. Alternatively spliced transcript variants have been reported; one of the variants lacks an internal exon and is considered non-coding, and the other variants encode the same protein. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.0709306E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSPO	NM_000714.6	c.439A>G	p.Thr147Ala	missense_variant	4/4	ENST00000337554.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPO	ENST00000337554.8	c.439A>G	p.Thr147Ala	missense_variant	4/4	1	NM_000714.6	P1
TSPO	ENST00000583777.5	c.127A>G	p.Thr43Ala	missense_variant	3/3	1
TSPO	ENST00000329563.8	c.439A>G	p.Thr147Ala	missense_variant	4/4	3		P1
TSPO	ENST00000396265.4	c.439A>G	p.Thr147Ala	missense_variant	4/4	5		P1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113905 AN: 152134 Hom.: 43087 Cov.: 35

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.759

GnomAD3 exomes AF: 0.758 AC: 164158 AN: 216438 Hom.: 63350 AF XY: 0.755 AC XY: 88465 AN XY: 117106

Gnomad AFR exome AF: 0.803

Gnomad AMR exome AF: 0.863

Gnomad ASJ exome AF: 0.702

Gnomad EAS exome AF: 0.977

Gnomad SAS exome AF: 0.842

Gnomad FIN exome AF: 0.672

Gnomad NFE exome AF: 0.681

Gnomad OTH exome AF: 0.734

GnomAD4 exome AF: 0.709 AC: 1020986 AN: 1440874 Hom.: 365559 Cov.: 83 AF XY: 0.712 AC XY: 509157 AN XY: 714894

Gnomad4 AFR exome AF: 0.811

Gnomad4 AMR exome AF: 0.855

Gnomad4 ASJ exome AF: 0.700

Gnomad4 EAS exome AF: 0.972

Gnomad4 SAS exome AF: 0.842

Gnomad4 FIN exome AF: 0.682

Gnomad4 NFE exome AF: 0.681

Gnomad4 OTH exome AF: 0.728

GnomAD4 genome AF: 0.749 AC: 114025 AN: 152252 Hom.: 43147 Cov.: 35 AF XY: 0.752 AC XY: 55990 AN XY: 74446

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.761

Alfa AF: 0.704 Hom.: 54604

Bravo AF: 0.762

TwinsUK AF: 0.672 AC: 2492

ALSPAC AF: 0.687 AC: 2649

ESP6500AA AF: 0.802 AC: 3526

ESP6500EA AF: 0.687 AC: 5905

ExAC AF: 0.738 AC: 88110

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.71	T
BayesDel_noAF	Benign	-0.64
Cadd	Benign	14
Dann	Benign	0.65
DEOGEN2	Benign	0.036	T;.;T;T
Eigen	Benign	-1.2
Eigen_PC	Benign	-0.96
FATHMM_MKL	Benign	0.15	N
MetaRNN	Benign	0.0000011	T;T;T;T
MetaSVM	Benign	-0.97	T
MutationTaster	Benign	1.0	P;P;P;P
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	3.7	N;.;N;.
REVEL	Benign	0.16
Sift	Benign	1.0	T;.;T;.
Sift4G	Benign	1.0	T;T;T;T
Polyphen		0.0	B;.;B;B
Vest4		0.14
MPC		0.21
ClinPred		0.021	T
GERP RS		3.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.097
gMVP		0.60

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

Other links and lift over

dbSNP: rs6971; hg19: chr22-43558926; COSMIC: COSV53355454; COSMIC: COSV53355454;